Starting phenix.real_space_refine
on Wed Jul  1 22:17:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e94_47768/07_2026/9e94_47768.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e94_47768/07_2026/9e94_47768.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e94_47768/07_2026/9e94_47768.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e94_47768/07_2026/9e94_47768.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e94_47768/07_2026/9e94_47768.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e94_47768/07_2026/9e94_47768.map"
  }
  resolution = 3.67
  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=   0.003 sd=   0.032
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: 5
    Type Number    sf(0)   Gaussians
     K       3      8.98       5
     S      10      5.16       5
     C    2266      2.51       5
     N     532      2.21       5
     O     570      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3381
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1654
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 210}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1654
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 210}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "A"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 50
          Ad-hoc single atom residues: {'  K': 2}
          Unusual residues: {'D10': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 20
          Ad-hoc single atom residues: {'  K': 1}
          Unusual residues: {'D10': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 1
  Time building chain proxies: 0.98, per 1000 atoms: 0.29
  Number of scatterers: 3381
  At special positions: 0
  Unit cell: (68.06, 86.32, 68.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       3     19.00
     S      10     16.00
     O     570      8.00
     N     532      7.00
     C    2266      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: 0.28
  Conformation dependent library (CDL) restraints added in 126.1 milliseconds
  

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  820

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      75.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 37
      removed outlier: 3.577A  pdb=" N   ARG A  27 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      Proline residue:  A  31  - end of helix
      removed outlier: 4.288A  pdb=" N   ARG A  37 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 48
    Processing helix  chain 'A' and resid 56 through 67
    Processing helix  chain 'A' and resid 92 through 105
    Processing helix  chain 'A' and resid 116 through 130
    Processing helix  chain 'A' and resid 131 through 149
    Processing helix  chain 'A' and resid 172 through 179
    Processing helix  chain 'A' and resid 180 through 185
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 200 through 213
    Processing helix  chain 'A' and resid 231 through 257
    Processing helix  chain 'B' and resid 8 through 37
      removed outlier: 3.576A  pdb=" N   ARG B  27 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      Proline residue:  B  31  - end of helix
      removed outlier: 4.288A  pdb=" N   ARG B  37 " --> pdb=" O   GLU B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 48
    Processing helix  chain 'B' and resid 56 through 67
    Processing helix  chain 'B' and resid 92 through 105
    Processing helix  chain 'B' and resid 116 through 130
    Processing helix  chain 'B' and resid 131 through 149
    Processing helix  chain 'B' and resid 172 through 179
    Processing helix  chain 'B' and resid 180 through 185
    Processing helix  chain 'B' and resid 187 through 196
    Processing helix  chain 'B' and resid 200 through 213
    Processing helix  chain 'B' and resid 231 through 257

    234 hydrogen bonds defined for protein.
    702 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.39

  Time building geometry restraints manager: 0.39 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: 928
        1.34 -     1.46: 615
        1.46 -     1.57: 1888
        1.57 -     1.69: 0
        1.69 -     1.80: 14
  Bond restraints: 3445
  Sorted by residual:
  bond pdb=" CG  LEU A 253 "
       pdb=" CD1 LEU A 253 "
    ideal  model  delta    sigma   weight residual
    1.521  1.418  0.103 3.30e-02 9.18e+02 9.65e+00
  bond pdb=" C   ALA B  56 "
       pdb=" N   PRO B  57 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 1.51e-02 4.39e+03 9.63e+00
  bond pdb=" CG  LEU B 253 "
       pdb=" CD1 LEU B 253 "
    ideal  model  delta    sigma   weight residual
    1.521  1.419  0.102 3.30e-02 9.18e+02 9.57e+00
  bond pdb=" C   ALA A  56 "
       pdb=" N   PRO A  57 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.046 1.51e-02 4.39e+03 9.38e+00
  bond pdb=" CG  LEU A 103 "
       pdb=" CD2 LEU A 103 "
    ideal  model  delta    sigma   weight residual
    1.521  1.432  0.089 3.30e-02 9.18e+02 7.23e+00
  ... (remaining 3440 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 4392
        3.21 -     6.42: 234
        6.42 -     9.64: 43
        9.64 -    12.85: 8
       12.85 -    16.06: 3
  Bond angle restraints: 4680
  Sorted by residual:
  angle pdb=" OG1 THR A 106 "
        pdb=" CB  THR A 106 "
        pdb=" CG2 THR A 106 "
      ideal   model   delta    sigma   weight residual
     109.30   93.95   15.35 2.00e+00 2.50e-01 5.89e+01
  angle pdb=" OG1 THR B 106 "
        pdb=" CB  THR B 106 "
        pdb=" CG2 THR B 106 "
      ideal   model   delta    sigma   weight residual
     109.30   93.99   15.31 2.00e+00 2.50e-01 5.86e+01
  angle pdb=" C   LEU A 103 "
        pdb=" N   ILE A 104 "
        pdb=" CA  ILE A 104 "
      ideal   model   delta    sigma   weight residual
     122.77  117.03    5.74 1.05e+00 9.07e-01 2.99e+01
  angle pdb=" C   LEU B 103 "
        pdb=" N   ILE B 104 "
        pdb=" CA  ILE B 104 "
      ideal   model   delta    sigma   weight residual
     122.77  117.06    5.71 1.05e+00 9.07e-01 2.96e+01
  angle pdb=" C4  D10 A 405 "
        pdb=" C5  D10 A 405 "
        pdb=" C6  D10 A 405 "
      ideal   model   delta    sigma   weight residual
     113.31  129.37  -16.06 3.00e+00 1.11e-01 2.87e+01
  ... (remaining 4675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.94: 1729
       13.94 -    27.89: 201
       27.89 -    41.83: 57
       41.83 -    55.77: 4
       55.77 -    69.71: 10
  Dihedral angle restraints: 2001
    sinusoidal: 729
      harmonic: 1272
  Sorted by residual:
  dihedral pdb=" CD  ARG B  71 "
           pdb=" NE  ARG B  71 "
           pdb=" CZ  ARG B  71 "
           pdb=" NH1 ARG B  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   52.86  -52.86     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CD  ARG A  71 "
           pdb=" NE  ARG A  71 "
           pdb=" CZ  ARG A  71 "
           pdb=" NH1 ARG A  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   52.81  -52.81     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CA  THR A 182 "
           pdb=" C   THR A 182 "
           pdb=" N   VAL A 183 "
           pdb=" CA  VAL A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.59   22.41     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 1998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 470
       0.106 -    0.212: 92
       0.212 -    0.318: 10
       0.318 -    0.424: 2
       0.424 -    0.530: 2
  Chirality restraints: 576
  Sorted by residual:
  chirality pdb=" CG  LEU A 103 "
            pdb=" CB  LEU A 103 "
            pdb=" CD1 LEU A 103 "
            pdb=" CD2 LEU A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.06   -0.53 2.00e-01 2.50e+01 7.02e+00
  chirality pdb=" CG  LEU B 103 "
            pdb=" CB  LEU B 103 "
            pdb=" CD1 LEU B 103 "
            pdb=" CD2 LEU B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.06   -0.53 2.00e-01 2.50e+01 7.02e+00
  chirality pdb=" CB  VAL B 252 "
            pdb=" CA  VAL B 252 "
            pdb=" CG1 VAL B 252 "
            pdb=" CG2 VAL B 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.22   -0.41 2.00e-01 2.50e+01 4.27e+00
  ... (remaining 573 not shown)

  Planarity restraints: 566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  71 "    0.712 9.50e-02 1.11e+02   3.20e-01 7.32e+01
        pdb=" NE  ARG B  71 "   -0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  71 "    0.050 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  71 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  71 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  71 "    0.710 9.50e-02 1.11e+02   3.20e-01 7.31e+01
        pdb=" NE  ARG A  71 "   -0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  71 "    0.050 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  71 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  71 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 109 "    0.001 2.00e-02 2.50e+03   3.78e-02 2.86e+01
        pdb=" CG  TYR A 109 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 109 "    0.073 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 109 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 109 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 109 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 109 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A 109 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 563 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.67: 84
        2.67 -     3.28: 3495
        3.28 -     3.90: 6326
        3.90 -     4.52: 8082
        4.52 -     5.14: 12426
  Nonbonded interactions: 30413
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 107 "
            pdb=" K     K A 406 "
     model   vdw
     2.047 3.590
  nonbonded pdb=" O   LEU B 217 "
            pdb=" K     K A 407 "
     model   vdw
     2.121 3.590
  nonbonded pdb=" O   THR B 106 "
            pdb=" K     K B 401 "
     model   vdw
     2.248 3.590
  nonbonded pdb=" O   LEU A 217 "
            pdb=" K     K A 407 "
     model   vdw
     2.339 3.590
  nonbonded pdb=" O   GLY A  73 "
            pdb=" NH2 ARG B  44 "
     model   vdw
     2.368 3.120
  ... (remaining 30408 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' and (resid 5 through 261 or resid 402 through 403))
  selection = (chain 'B' and (resid 5 through 261 or resid 402 through 403))
}

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:             1.150
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.980
  Find NCS groups from input model:        0.060
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
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      :  0.010   0.103   3445  Z= 0.455
  Angle     :  1.694  16.060   4680  Z= 0.911
  Chirality :  0.090   0.530    576
  Planarity :  0.025   0.320    566
  Dihedral  : 14.022  69.715   1181
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.49 %
  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: -4.00 (0.32), residues: 428
  helix: -1.66 (0.24), residues: 326
  sheet:  None (None), residues: 0
  loop : -5.64 (0.31), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.058   0.008   ARG A  71 
 TYR   0.073   0.005   TYR B 109 
 PHE   0.064   0.008   PHE A 256 
 TRP   0.047   0.007   TRP B  91 
 HIS   0.004   0.002   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01011 /  0.46 ( 3445)
  covalent geometry    : angle       1.69363 /  0.91 ( 4680)
  hydrogen bonds       : bond        0.10782 /  7.51 (  234)
  hydrogen bonds       : angle       6.14224 /  4.34 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1155
  time to fit residues: 13.0839
Evaluate side-chains
  65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0870
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 254 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.205761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.161537 restraints weight = 3803.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.164122 restraints weight = 3983.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.165848 restraints weight = 2791.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.166223 restraints weight = 2301.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.166487 restraints weight = 2138.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   3445  Z= 0.164
  Angle     :  0.782   9.482   4680  Z= 0.385
  Chirality :  0.043   0.145    576
  Planarity :  0.006   0.037    566
  Dihedral  :  6.838  54.631    521
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  3.97 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 10.84 %
    Favored  : 86.45 %
  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: -1.27 (0.39), residues: 428
  helix:  0.33 (0.27), residues: 336
  sheet:  None (None), residues: 0
  loop : -5.32 (0.34), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  65 
 TYR   0.019   0.002   TYR B 109 
 PHE   0.015   0.002   PHE A 207 
 TRP   0.008   0.001   TRP A  91 
 HIS   0.003   0.001   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00373 /  0.16 ( 3445)
  covalent geometry    : angle       0.78238 /  0.38 ( 4680)
  hydrogen bonds       : bond        0.04527 /  3.02 (  234)
  hydrogen bonds       : angle       4.27008 /  3.04 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 ARG cc_start: 0.7009 (mpp80) cc_final: 0.6421 (mtm110)
REVERT: A   29 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7273 (tm-30)
REVERT: B  104 ILE cc_start: 0.8184 (tt) cc_final: 0.7837 (tt)
  outliers start: 9
  outliers final: 6
  residues processed: 64
  average time/residue: 0.1300
  time to fit residues: 9.4095
Evaluate side-chains
  53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  208 CYS
Chi-restraints excluded: chain B residue  231 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 36 optimal weight:    0.0020
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0970
   chunk 25 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.2986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.210478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.168325 restraints weight = 3904.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.169936 restraints weight = 3853.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.170241 restraints weight = 3497.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.170342 restraints weight = 3287.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.170490 restraints weight = 3313.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3445  Z= 0.120
  Angle     :  0.597   6.646   4680  Z= 0.300
  Chirality :  0.038   0.128    576
  Planarity :  0.005   0.035    566
  Dihedral  :  6.181  53.501    521
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 12.05 %
    Favored  : 83.73 %
  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:  0.30 (0.42), residues: 428
  helix:  1.39 (0.29), residues: 336
  sheet:  None (None), residues: 0
  loop : -4.53 (0.47), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  65 
 TYR   0.014   0.001   TYR B 109 
 PHE   0.011   0.001   PHE B 185 
 TRP   0.005   0.001   TRP B  91 
 HIS   0.001   0.000   HIS A  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 3445)
  covalent geometry    : angle       0.59729 /  0.30 ( 4680)
  hydrogen bonds       : bond        0.03670 /  2.45 (  234)
  hydrogen bonds       : angle       3.73866 /  2.66 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A   27 ARG cc_start: 0.6868 (mpp80) cc_final: 0.6281 (mtm110)
REVERT: B  104 ILE cc_start: 0.8350 (tt) cc_final: 0.8035 (tt)
REVERT: B  228 GLN cc_start: 0.6779 (tp40) cc_final: 0.6558 (mm-40)
  outliers start: 14
  outliers final: 7
  residues processed: 61
  average time/residue: 0.1183
  time to fit residues: 8.2052
Evaluate side-chains
  52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  256 PHE
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  231 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0370
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   overall best weight:    0.6458

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.204602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.166984 restraints weight = 3840.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.164174 restraints weight = 4324.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.163883 restraints weight = 5045.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.164470 restraints weight = 4777.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.164465 restraints weight = 4131.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3445  Z= 0.142
  Angle     :  0.611   8.135   4680  Z= 0.301
  Chirality :  0.038   0.121    576
  Planarity :  0.005   0.037    566
  Dihedral  :  5.988  52.516    521
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 13.55 %
    Favored  : 81.33 %
  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:  1.09 (0.43), residues: 428
  helix:  1.89 (0.29), residues: 336
  sheet:  None (None), residues: 0
  loop : -3.99 (0.56), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  65 
 TYR   0.011   0.001   TYR B 109 
 PHE   0.014   0.002   PHE B 185 
 TRP   0.011   0.002   TRP B  91 
 HIS   0.002   0.001   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 3445)
  covalent geometry    : angle       0.61135 /  0.30 ( 4680)
  hydrogen bonds       : bond        0.03752 /  2.48 (  234)
  hydrogen bonds       : angle       3.56692 /  2.54 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   24 LEU cc_start: 0.6780 (tp) cc_final: 0.6486 (tt)
REVERT: A   27 ARG cc_start: 0.7149 (mpp80) cc_final: 0.6559 (mtm110)
REVERT: B   44 ARG cc_start: 0.6725 (ttt90) cc_final: 0.6472 (ttt90)
REVERT: B  213 SER cc_start: 0.8759 (t) cc_final: 0.8531 (m)
REVERT: B  228 GLN cc_start: 0.6900 (tp40) cc_final: 0.6648 (mm-40)
  outliers start: 17
  outliers final: 9
  residues processed: 60
  average time/residue: 0.1075
  time to fit residues: 7.3210
Evaluate side-chains
  54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  256 PHE
Chi-restraints excluded: chain B residue   29 GLU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  231 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 26 optimal weight:    0.2980
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.205243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.172928 restraints weight = 3823.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.169372 restraints weight = 6495.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.169470 restraints weight = 6363.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.168724 restraints weight = 5369.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.169003 restraints weight = 4595.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.4499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3445  Z= 0.128
  Angle     :  0.572   7.959   4680  Z= 0.283
  Chirality :  0.038   0.120    576
  Planarity :  0.005   0.042    566
  Dihedral  :  5.830  50.517    521
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 13.86 %
    Favored  : 81.93 %
  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:  1.49 (0.43), residues: 428
  helix:  2.11 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -3.69 (0.58), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  37 
 TYR   0.009   0.001   TYR B  17 
 PHE   0.015   0.002   PHE B 209 
 TRP   0.018   0.001   TRP B  91 
 HIS   0.001   0.000   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 3445)
  covalent geometry    : angle       0.57220 /  0.28 ( 4680)
  hydrogen bonds       : bond        0.03577 /  2.39 (  234)
  hydrogen bonds       : angle       3.51422 /  2.52 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A   27 ARG cc_start: 0.7119 (mpp80) cc_final: 0.6524 (mtm110)
REVERT: A  111 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.5553 (t80)
REVERT: B   74 ARG cc_start: 0.7252 (ptm160) cc_final: 0.6864 (ptm160)
REVERT: B  213 SER cc_start: 0.8768 (t) cc_final: 0.8519 (m)
  outliers start: 14
  outliers final: 10
  residues processed: 53
  average time/residue: 0.1307
  time to fit residues: 7.8282
Evaluate side-chains
  54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  256 PHE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   29 GLU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  231 ARG
Chi-restraints excluded: chain B residue  233 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 39 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.203034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.159454 restraints weight = 3825.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.160983 restraints weight = 3653.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.161035 restraints weight = 3409.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.160991 restraints weight = 3300.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.160948 restraints weight = 3430.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3445  Z= 0.139
  Angle     :  0.623  11.032   4680  Z= 0.296
  Chirality :  0.038   0.123    576
  Planarity :  0.005   0.044    566
  Dihedral  :  5.799  50.213    521
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 14.16 %
    Favored  : 81.63 %
  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:  1.74 (0.43), residues: 428
  helix:  2.25 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -3.45 (0.61), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  65 
 TYR   0.015   0.001   TYR A 220 
 PHE   0.010   0.002   PHE A 122 
 TRP   0.008   0.001   TRP B  91 
 HIS   0.001   0.000   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 3445)
  covalent geometry    : angle       0.62254 /  0.30 ( 4680)
  hydrogen bonds       : bond        0.03616 /  2.40 (  234)
  hydrogen bonds       : angle       3.55285 /  2.54 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   27 ARG cc_start: 0.7051 (mpp80) cc_final: 0.6383 (mtm110)
REVERT: A  111 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.5796 (t80)
REVERT: A  220 TYR cc_start: 0.8592 (m-10) cc_final: 0.8115 (m-80)
REVERT: B   74 ARG cc_start: 0.6976 (ptm160) cc_final: 0.6611 (ptm160)
REVERT: B  213 SER cc_start: 0.8907 (t) cc_final: 0.8617 (m)
REVERT: B  231 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7284 (tpt-90)
  outliers start: 14
  outliers final: 9
  residues processed: 55
  average time/residue: 0.1097
  time to fit residues: 6.8251
Evaluate side-chains
  50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  256 PHE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   29 GLU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  231 ARG
Chi-restraints excluded: chain B residue  233 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.2584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.195837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.155644 restraints weight = 3887.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.152860 restraints weight = 3887.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.152738 restraints weight = 3817.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.152582 restraints weight = 3923.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.152642 restraints weight = 3719.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.5144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   3445  Z= 0.203
  Angle     :  0.711  11.192   4680  Z= 0.343
  Chirality :  0.042   0.154    576
  Planarity :  0.005   0.041    566
  Dihedral  :  6.342  49.860    521
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 14.16 %
    Favored  : 81.33 %
  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:  1.59 (0.43), residues: 428
  helix:  2.00 (0.28), residues: 342
  sheet:  None (None), residues: 0
  loop : -3.06 (0.67), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  65 
 TYR   0.012   0.001   TYR A 220 
 PHE   0.017   0.002   PHE A 122 
 TRP   0.014   0.002   TRP B  91 
 HIS   0.002   0.001   HIS B 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00498 /  0.20 ( 3445)
  covalent geometry    : angle       0.71093 /  0.34 ( 4680)
  hydrogen bonds       : bond        0.04226 /  2.80 (  234)
  hydrogen bonds       : angle       3.75323 /  2.71 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 ARG cc_start: 0.7249 (mpp80) cc_final: 0.6598 (mtm110)
REVERT: A   29 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7441 (tm-30)
REVERT: A  111 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6127 (t80)
REVERT: B  231 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7671 (tpt-90)
  outliers start: 15
  outliers final: 11
  residues processed: 50
  average time/residue: 0.1078
  time to fit residues: 6.1528
Evaluate side-chains
  51 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 GLU
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  256 PHE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   29 GLU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  231 ARG
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  256 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.188298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.144800 restraints weight = 3772.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.146815 restraints weight = 4220.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.147224 restraints weight = 3475.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.147419 restraints weight = 2729.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.148250 restraints weight = 2435.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.5331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3445  Z= 0.137
  Angle     :  0.629  10.263   4680  Z= 0.298
  Chirality :  0.038   0.124    576
  Planarity :  0.005   0.048    566
  Dihedral  :  5.910  44.927    521
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 13.86 %
    Favored  : 81.33 %
  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:  1.93 (0.43), residues: 428
  helix:  2.35 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -3.22 (0.64), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  65 
 TYR   0.012   0.001   TYR A 220 
 PHE   0.013   0.002   PHE B 209 
 TRP   0.009   0.001   TRP B  91 
 HIS   0.001   0.000   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 3445)
  covalent geometry    : angle       0.62910 /  0.30 ( 4680)
  hydrogen bonds       : bond        0.03617 /  2.41 (  234)
  hydrogen bonds       : angle       3.60362 /  2.57 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.8403 (tp) cc_final: 0.8192 (tp)
REVERT: A   27 ARG cc_start: 0.7282 (mpp80) cc_final: 0.6628 (mtm110)
REVERT: A   29 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7779 (tm-30)
REVERT: A  111 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6194 (t80)
REVERT: B   44 ARG cc_start: 0.7490 (tpp80) cc_final: 0.6887 (ttt90)
REVERT: B  231 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7598 (tpt-90)
  outliers start: 16
  outliers final: 12
  residues processed: 50
  average time/residue: 0.1173
  time to fit residues: 6.7641
Evaluate side-chains
  52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 GLU
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  256 PHE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   29 GLU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  231 ARG
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  256 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0970
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.5778

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.190244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.141553 restraints weight = 3680.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.146453 restraints weight = 2746.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.147368 restraints weight = 2193.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.148407 restraints weight = 1944.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.148899 restraints weight = 1851.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.5496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3445  Z= 0.131
  Angle     :  0.628  10.246   4680  Z= 0.296
  Chirality :  0.037   0.120    576
  Planarity :  0.005   0.063    566
  Dihedral  :  5.667  43.180    521
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 15.36 %
    Favored  : 80.12 %
  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:  2.13 (0.43), residues: 428
  helix:  2.55 (0.28), residues: 336
  sheet:  None (None), residues: 0
  loop : -3.24 (0.63), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  65 
 TYR   0.009   0.001   TYR A 220 
 PHE   0.011   0.001   PHE A 207 
 TRP   0.006   0.001   TRP B  91 
 HIS   0.002   0.000   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 ( 3445)
  covalent geometry    : angle       0.62793 /  0.30 ( 4680)
  hydrogen bonds       : bond        0.03482 /  2.34 (  234)
  hydrogen bonds       : angle       3.47231 /  2.46 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.8393 (tp) cc_final: 0.8178 (tp)
REVERT: A   27 ARG cc_start: 0.7088 (mpp80) cc_final: 0.6412 (mtm110)
REVERT: A   29 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7742 (tm-30)
REVERT: A  111 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6165 (t80)
REVERT: B  194 HIS cc_start: 0.6601 (t-90) cc_final: 0.5764 (t-170)
REVERT: B  231 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7347 (tpt-90)
  outliers start: 15
  outliers final: 11
  residues processed: 51
  average time/residue: 0.1161
  time to fit residues: 6.8051
Evaluate side-chains
  53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 GLU
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  256 PHE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   29 GLU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  231 ARG
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  256 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.189163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.139979 restraints weight = 3746.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.143180 restraints weight = 2772.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.144954 restraints weight = 2315.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.146297 restraints weight = 2079.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.146784 restraints weight = 1951.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.5614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3445  Z= 0.141
  Angle     :  0.643  10.192   4680  Z= 0.303
  Chirality :  0.039   0.138    576
  Planarity :  0.005   0.058    566
  Dihedral  :  5.640  42.040    521
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 15.66 %
    Favored  : 80.12 %
  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:  2.23 (0.43), residues: 428
  helix:  2.56 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -3.08 (0.64), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  65 
 TYR   0.008   0.001   TYR B 230 
 PHE   0.011   0.002   PHE A 122 
 TRP   0.006   0.001   TRP B  91 
 HIS   0.001   0.000   HIS B 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 3445)
  covalent geometry    : angle       0.64301 /  0.30 ( 4680)
  hydrogen bonds       : bond        0.03581 /  2.39 (  234)
  hydrogen bonds       : angle       3.49554 /  2.48 (  702)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.8403 (tp) cc_final: 0.8191 (tp)
REVERT: A   27 ARG cc_start: 0.7104 (mpp80) cc_final: 0.6432 (mtm110)
REVERT: A   29 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7723 (tm-30)
REVERT: A  111 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6136 (t80)
REVERT: B   74 ARG cc_start: 0.7165 (ptm160) cc_final: 0.6847 (ptm160)
REVERT: B  194 HIS cc_start: 0.6627 (t-90) cc_final: 0.5750 (t-170)
REVERT: B  231 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7366 (tpt-90)
  outliers start: 14
  outliers final: 11
  residues processed: 49
  average time/residue: 0.0895
  time to fit residues: 5.0454
Evaluate side-chains
  51 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 GLU
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  256 PHE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   29 GLU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  231 ARG
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  256 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 39 optimal weight:    0.1980
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.190731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.146419 restraints weight = 3816.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.143385 restraints weight = 4218.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.146206 restraints weight = 3751.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.146925 restraints weight = 2843.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.147031 restraints weight = 2613.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.5695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3445  Z= 0.126
  Angle     :  0.629  10.072   4680  Z= 0.294
  Chirality :  0.038   0.124    576
  Planarity :  0.005   0.058    566
  Dihedral  :  5.463  39.167    521
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 15.96 %
    Favored  : 79.82 %
  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:  2.38 (0.43), residues: 428
  helix:  2.71 (0.28), residues: 336
  sheet:  None (None), residues: 0
  loop : -3.13 (0.64), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  65 
 TYR   0.009   0.001   TYR A 220 
 PHE   0.010   0.001   PHE A 207 
 TRP   0.006   0.001   TRP B  91 
 HIS   0.001   0.000   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 3445)
  covalent geometry    : angle       0.62867 /  0.29 ( 4680)
  hydrogen bonds       : bond        0.03412 /  2.28 (  234)
  hydrogen bonds       : angle       3.44435 /  2.44 (  702)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 794.23 seconds
wall clock time: 14 minutes 23.75 seconds (863.75 seconds total)