Starting phenix.real_space_refine
on Mon Jan 13 13:28:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y84_39032/01_2025/8y84_39032.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y84_39032/01_2025/8y84_39032.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y84_39032/01_2025/8y84_39032.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y84_39032/01_2025/8y84_39032.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y84_39032/01_2025/8y84_39032.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y84_39032/01_2025/8y84_39032.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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: 4
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    1453      2.51       5
     N     330      2.21       5
     O     372      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 2168
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 331
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 1, 'TRANS': 37}
    Chain: "B"
      Number of atoms: 1227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 158, 1227
          Classifications: {'peptide': 158}
          Link IDs: {'PTRANS': 1, 'TRANS': 156}
    Chain: "C"
      Number of atoms: 301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 301
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "G"
      Number of atoms: 274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 274
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.47, per 1000 atoms: 1.14
  Number of scatterers: 2168
  At special positions: 0
  Unit cell: (64.2, 68.48, 73.83, 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      13     16.00
     O     372      8.00
     N     330      7.00
     C    1453      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  25 " - pdb=" SG  CYS G  25 " distance=2.03

  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: 0.55
  Conformation dependent library (CDL) restraints added in 267.1 milliseconds
  

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  506

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 0 sheets defined
      88.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 200 through 204
      removed outlier: 3.568A  pdb=" N   LEU A 203 " --> pdb=" O   TYR A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 234
      removed outlier: 3.546A  pdb=" N   SER A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 216 " --> pdb=" O   VAL A 212 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   THR A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLN A 228 " --> pdb=" O   SER A 224 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A 232 " --> pdb=" O   GLN A 228 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 233 " --> pdb=" O   PHE A 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 56
    Processing helix  chain 'B' and resid 57 through 83
      removed outlier: 4.277A  pdb=" N   GLN B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 98
    Processing helix  chain 'B' and resid 99 through 122
      removed outlier: 3.747A  pdb=" N   LEU B 107 " --> pdb=" O   TRP B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 161
      removed outlier: 4.176A  pdb=" N   TYR B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 205
      removed outlier: 3.553A  pdb=" N   PHE B 172 " --> pdb=" O   ASP B 168 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU B 187 " --> pdb=" O   MET B 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 58
      removed outlier: 3.686A  pdb=" N   ARG C  58 " --> pdb=" O   ASP C  54 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 25 through 56
      removed outlier: 3.708A  pdb=" N   LEU G  32 " --> pdb=" O   LEU G  28 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE G  48 " --> pdb=" O   CYS G  44 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLN G  49 " --> pdb=" O   ARG G  45 " (cutoff:3.500A)

    182 hydrogen bonds defined for protein.
    543 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: 0.54

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 363
        1.33 -     1.45: 558
        1.45 -     1.57: 1273
        1.57 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 2210
  Sorted by residual:
  bond pdb=" CAX Y01 B 601 "
       pdb=" OAH Y01 B 601 "
    ideal  model  delta    sigma   weight residual
    1.248  1.342 -0.094 2.00e-02 2.50e+03 2.20e+01
  bond pdb=" N   GLU A 199 "
       pdb=" CA  GLU A 199 "
    ideal  model  delta    sigma   weight residual
    1.462  1.529 -0.067 1.46e-02 4.69e+03 2.11e+01
  bond pdb=" C   ILE A 198 "
       pdb=" N   GLU A 199 "
    ideal  model  delta    sigma   weight residual
    1.333  1.369 -0.036 1.45e-02 4.76e+03 6.28e+00
  bond pdb=" CAX Y01 B 601 "
       pdb=" OAF Y01 B 601 "
    ideal  model  delta    sigma   weight residual
    1.247  1.207  0.040 2.00e-02 2.50e+03 4.02e+00
  bond pdb=" C   PHE A 207 "
       pdb=" N   PRO A 208 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.046 2.34e-02 1.83e+03 3.90e+00
  ... (remaining 2205 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 2922
        2.98 -     5.95: 57
        5.95 -     8.93: 18
        8.93 -    11.91: 2
       11.91 -    14.88: 1
  Bond angle restraints: 3000
  Sorted by residual:
  angle pdb=" N   ILE C  55 "
        pdb=" CA  ILE C  55 "
        pdb=" C   ILE C  55 "
      ideal   model   delta    sigma   weight residual
     113.22  107.51    5.71 1.23e+00 6.61e-01 2.16e+01
  angle pdb=" C   VAL B 127 "
        pdb=" N   ARG B 128 "
        pdb=" CA  ARG B 128 "
      ideal   model   delta    sigma   weight residual
     121.54  129.74   -8.20 1.91e+00 2.74e-01 1.84e+01
  angle pdb=" CA  LEU B  58 "
        pdb=" CB  LEU B  58 "
        pdb=" CG  LEU B  58 "
      ideal   model   delta    sigma   weight residual
     116.30  131.18  -14.88 3.50e+00 8.16e-02 1.81e+01
  angle pdb=" CA  ILE A 198 "
        pdb=" C   ILE A 198 "
        pdb=" N   GLU A 199 "
      ideal   model   delta    sigma   weight residual
     116.20  123.92   -7.72 2.00e+00 2.50e-01 1.49e+01
  angle pdb=" O   ILE A 198 "
        pdb=" C   ILE A 198 "
        pdb=" N   GLU A 199 "
      ideal   model   delta    sigma   weight residual
     123.00  117.35    5.65 1.60e+00 3.91e-01 1.25e+01
  ... (remaining 2995 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.17: 1142
       15.17 -    30.33: 151
       30.33 -    45.49: 38
       45.49 -    60.66: 14
       60.66 -    75.82: 2
  Dihedral angle restraints: 1347
    sinusoidal: 564
      harmonic: 783
  Sorted by residual:
  dihedral pdb=" CB  CYS C  25 "
           pdb=" SG  CYS C  25 "
           pdb=" SG  CYS G  25 "
           pdb=" CB  CYS G  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.37  -54.37     1      1.00e+01 1.00e-02 4.01e+01
  dihedral pdb=" CA  MET B 183 "
           pdb=" C   MET B 183 "
           pdb=" N   LEU B 184 "
           pdb=" CA  LEU B 184 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.10   23.90     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  GLU A 199 "
           pdb=" C   GLU A 199 "
           pdb=" N   TYR A 200 "
           pdb=" CA  TYR A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.70   23.30     0      5.00e+00 4.00e-02 2.17e+01
  ... (remaining 1344 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 304
       0.066 -    0.132: 51
       0.132 -    0.198: 10
       0.198 -    0.264: 4
       0.264 -    0.330: 2
  Chirality restraints: 371
  Sorted by residual:
  chirality pdb=" CBH Y01 B 601 "
            pdb=" CAT Y01 B 601 "
            pdb=" CAZ Y01 B 601 "
            pdb=" CBF Y01 B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.52   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CBG Y01 B 601 "
            pdb=" CAQ Y01 B 601 "
            pdb=" CBD Y01 B 601 "
            pdb=" CBI Y01 B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.61    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CBD Y01 B 601 "
            pdb=" CAK Y01 B 601 "
            pdb=" CBF Y01 B 601 "
            pdb=" CBG Y01 B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.70    2.93   -0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 368 not shown)

  Planarity restraints: 350
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 198 "    0.015 2.00e-02 2.50e+03   2.95e-02 8.71e+00
        pdb=" C   ILE A 198 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ILE A 198 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLU A 199 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 101 "    0.013 2.00e-02 2.50e+03   2.57e-02 6.59e+00
        pdb=" C   PRO B 101 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   PRO B 101 "    0.016 2.00e-02 2.50e+03
        pdb=" N   PHE B 102 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 220 "    0.012 2.00e-02 2.50e+03   2.35e-02 5.52e+00
        pdb=" C   GLY A 220 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLY A 220 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A 221 "    0.014 2.00e-02 2.50e+03
  ... (remaining 347 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 539
        2.80 -     3.32: 2149
        3.32 -     3.85: 3728
        3.85 -     4.37: 4323
        4.37 -     4.90: 7381
  Nonbonded interactions: 18120
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C  35 "
            pdb=" OG1 THR G  40 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   THR B 174 "
            pdb=" OG1 THR B 178 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" O   VAL B  78 "
            pdb=" OG1 THR B  82 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   LEU B 184 "
            pdb=" OG1 THR B 188 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O   GLY B 170 "
            pdb=" OG1 THR B 174 "
     model   vdw
     2.381 3.040
  ... (remaining 18115 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 'C' and resid 24 through 57)
  selection = chain 'G'
}

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:             1.020
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.170
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
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      :  0.007   0.094   2210  Z= 0.426
  Angle     :  1.151  14.883   3000  Z= 0.571
  Chirality :  0.060   0.330    371
  Planarity :  0.006   0.038    350
  Dihedral  : 15.183  75.822    835
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.45), residues: 260
  helix: -0.99 (0.29), residues: 221
  sheet:  None (None), residues: 0
  loop : -0.09 (1.09), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 103 
 HIS   0.006   0.004   HIS A 226 
 PHE   0.026   0.002   PHE A 207 
 TYR   0.029   0.004   TYR G  43 
 ARG   0.011   0.001   ARG C  45 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.252 
Fit side-chains
REVERT: C   32 LEU cc_start: 0.8111 (tt) cc_final: 0.7906 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.7294
  time to fit residues: 20.6178
Evaluate side-chains
  25 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 18 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.157223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.134323 restraints weight = 2590.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.57
r_work: 0.3277 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2210  Z= 0.242
  Angle     :  0.603   5.676   3000  Z= 0.310
  Chirality :  0.039   0.119    371
  Planarity :  0.004   0.021    350
  Dihedral  : 10.870  58.752    358
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.05 %
    Favored  : 90.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.50), residues: 260
  helix:  0.44 (0.32), residues: 226
  sheet:  None (None), residues: 0
  loop : -0.21 (1.16), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B  50 
 HIS   0.002   0.001   HIS A 226 
 PHE   0.010   0.001   PHE B 102 
 TYR   0.024   0.002   TYR C  35 
 ARG   0.003   0.000   ARG C  45 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.8322 (mmt90) cc_final: 0.7999 (tpt-90)
REVERT: A  226 HIS cc_start: 0.7087 (t70) cc_final: 0.6711 (t-170)
REVERT: A  227 LYS cc_start: 0.7685 (ptmt) cc_final: 0.7405 (ptmm)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 0.9176
  time to fit residues: 28.4564
Evaluate side-chains
  30 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  183 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0980
   chunk 10 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.143554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.120198 restraints weight = 2651.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.64
r_work: 0.3225 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2210  Z= 0.261
  Angle     :  0.595   5.703   3000  Z= 0.306
  Chirality :  0.039   0.129    371
  Planarity :  0.003   0.018    350
  Dihedral  : 10.134  57.890    358
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 12.71 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.50), residues: 260
  helix:  0.82 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop :  0.00 (1.23), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B  50 
 HIS   0.002   0.001   HIS A 226 
 PHE   0.009   0.001   PHE B 102 
 TYR   0.023   0.002   TYR C  35 
 ARG   0.001   0.000   ARG B 128 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.8508 (mmt90) cc_final: 0.8178 (tpt-90)
REVERT: A  226 HIS cc_start: 0.7160 (t70) cc_final: 0.6766 (t-170)
REVERT: A  227 LYS cc_start: 0.7767 (ptmt) cc_final: 0.7557 (ptmm)
  outliers start: 2
  outliers final: 1
  residues processed: 27
  average time/residue: 0.8241
  time to fit residues: 23.1938
Evaluate side-chains
  26 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  165 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0570
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.3498

-------------------------------------------------------------------------------
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 = 0.3672 r_free = 0.3672 target = 0.146292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123318 restraints weight = 2640.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.60
r_work: 0.3271 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2210  Z= 0.189
  Angle     :  0.536   5.524   3000  Z= 0.277
  Chirality :  0.036   0.119    371
  Planarity :  0.003   0.018    350
  Dihedral  :  9.285  58.028    358
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 14.41 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.50), residues: 260
  helix:  1.28 (0.33), residues: 226
  sheet:  None (None), residues: 0
  loop :  0.23 (1.17), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B  50 
 HIS   0.001   0.001   HIS A 226 
 PHE   0.006   0.001   PHE B 102 
 TYR   0.018   0.002   TYR C  35 
 ARG   0.001   0.000   ARG B 128 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.8440 (mmt90) cc_final: 0.8080 (tpt-90)
REVERT: A  226 HIS cc_start: 0.7186 (t70) cc_final: 0.6829 (t-170)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 0.7669
  time to fit residues: 23.9783
Evaluate side-chains
  29 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain G residue   32 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 4 optimal weight:    0.1980
   chunk 15 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0970
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    0.4980
   chunk 7 optimal weight:    0.2980
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.3178

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.147518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.124715 restraints weight = 2628.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.59
r_work: 0.3304 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2210  Z= 0.181
  Angle     :  0.522   5.588   3000  Z= 0.271
  Chirality :  0.036   0.120    371
  Planarity :  0.003   0.017    350
  Dihedral  :  9.017  56.700    358
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.25 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.51), residues: 260
  helix:  1.54 (0.33), residues: 226
  sheet:  None (None), residues: 0
  loop :  0.46 (1.21), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B  50 
 HIS   0.001   0.001   HIS A 226 
 PHE   0.016   0.001   PHE A 207 
 TYR   0.018   0.002   TYR C  35 
 ARG   0.001   0.000   ARG B 128 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.8425 (mmt90) cc_final: 0.8045 (tpt-90)
REVERT: A  226 HIS cc_start: 0.7210 (t70) cc_final: 0.6842 (t-170)
  outliers start: 5
  outliers final: 3
  residues processed: 33
  average time/residue: 0.7417
  time to fit residues: 25.5543
Evaluate side-chains
  31 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain G residue   32 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.145002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.122497 restraints weight = 2669.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.58
r_work: 0.3251 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2210  Z= 0.228
  Angle     :  0.556   5.995   3000  Z= 0.288
  Chirality :  0.037   0.132    371
  Planarity :  0.003   0.018    350
  Dihedral  :  9.040  57.132    358
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.68 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.51), residues: 260
  helix:  1.52 (0.33), residues: 226
  sheet:  None (None), residues: 0
  loop :  0.38 (1.19), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP B  50 
 HIS   0.002   0.001   HIS A 226 
 PHE   0.020   0.001   PHE A 207 
 TYR   0.014   0.002   TYR B 100 
 ARG   0.001   0.000   ARG B 128 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.8469 (mmt90) cc_final: 0.8078 (tpt-90)
REVERT: A  226 HIS cc_start: 0.7169 (t70) cc_final: 0.6802 (t-170)
REVERT: C   29 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6698 (m-30)
REVERT: G   33 PHE cc_start: 0.7739 (m-80) cc_final: 0.7531 (m-80)
REVERT: G   40 THR cc_start: 0.8023 (m) cc_final: 0.7795 (m)
  outliers start: 6
  outliers final: 2
  residues processed: 32
  average time/residue: 0.7408
  time to fit residues: 24.6774
Evaluate side-chains
  28 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain G residue   32 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.141772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118827 restraints weight = 2690.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.63
r_work: 0.3208 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2210  Z= 0.288
  Angle     :  0.609   6.318   3000  Z= 0.310
  Chirality :  0.039   0.137    371
  Planarity :  0.003   0.018    350
  Dihedral  :  8.953  54.745    358
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.22 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.51), residues: 260
  helix:  1.32 (0.33), residues: 227
  sheet:  None (None), residues: 0
  loop :  0.38 (1.19), residues: 33

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.004   TRP B  50 
 HIS   0.002   0.001   HIS A 226 
 PHE   0.024   0.001   PHE A 207 
 TYR   0.016   0.002   TYR B 100 
 ARG   0.001   0.000   ARG B 128 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  226 HIS cc_start: 0.7203 (t70) cc_final: 0.6807 (t-170)
REVERT: B  167 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7698 (tt0)
REVERT: C   29 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6804 (m-30)
REVERT: G   40 THR cc_start: 0.8045 (m) cc_final: 0.7836 (m)
  outliers start: 6
  outliers final: 3
  residues processed: 29
  average time/residue: 0.6843
  time to fit residues: 20.7958
Evaluate side-chains
  30 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain G residue   32 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 7 optimal weight:    0.0970
   chunk 1 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    0.1980
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 22 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.144523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.122032 restraints weight = 2759.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.61
r_work: 0.3255 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2210  Z= 0.205
  Angle     :  0.570   7.354   3000  Z= 0.291
  Chirality :  0.037   0.129    371
  Planarity :  0.003   0.018    350
  Dihedral  :  8.577  55.788    358
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.92 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.51), residues: 260
  helix:  1.56 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop :  0.56 (1.29), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP B  50 
 HIS   0.001   0.001   HIS A 226 
 PHE   0.018   0.001   PHE A 207 
 TYR   0.015   0.001   TYR B 100 
 ARG   0.001   0.000   ARG B 128 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  226 HIS cc_start: 0.7159 (t70) cc_final: 0.6784 (t-170)
REVERT: G   40 THR cc_start: 0.7960 (m) cc_final: 0.7709 (m)
  outliers start: 4
  outliers final: 3
  residues processed: 31
  average time/residue: 0.5857
  time to fit residues: 19.1360
Evaluate side-chains
  31 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain G residue   32 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0980
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.156862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.134695 restraints weight = 2621.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.56
r_work: 0.3350 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2210  Z= 0.236
  Angle     :  0.607  11.974   3000  Z= 0.304
  Chirality :  0.037   0.134    371
  Planarity :  0.003   0.018    350
  Dihedral  :  8.645  57.529    358
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 21.19 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.51), residues: 260
  helix:  1.58 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop :  0.55 (1.28), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.004   TRP B  50 
 HIS   0.002   0.001   HIS A 226 
 PHE   0.020   0.001   PHE A 207 
 TYR   0.015   0.002   TYR B 100 
 ARG   0.001   0.000   ARG B 128 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  226 HIS cc_start: 0.7147 (t70) cc_final: 0.6732 (t-170)
REVERT: G   40 THR cc_start: 0.8064 (m) cc_final: 0.7823 (m)
  outliers start: 3
  outliers final: 2
  residues processed: 27
  average time/residue: 0.6463
  time to fit residues: 18.3543
Evaluate side-chains
  25 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  165 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0970
   chunk 2 optimal weight:    0.6980
   chunk 17 optimal weight:    0.1980
   chunk 19 optimal weight:    0.0770
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.3536

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.158163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.136438 restraints weight = 2577.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.54
r_work: 0.3279 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2210  Z= 0.212
  Angle     :  0.606  12.190   3000  Z= 0.301
  Chirality :  0.036   0.128    371
  Planarity :  0.003   0.018    350
  Dihedral  :  8.562  58.388    358
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 21.19 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.51), residues: 260
  helix:  1.71 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop :  0.65 (1.30), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.004   TRP B  50 
 HIS   0.002   0.001   HIS A 226 
 PHE   0.019   0.001   PHE A 207 
 TYR   0.015   0.001   TYR B 100 
 ARG   0.001   0.000   ARG B 128 

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.261 
Fit side-chains
REVERT: C   29 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6569 (m-30)
REVERT: G   40 THR cc_start: 0.7884 (m) cc_final: 0.7655 (m)
  outliers start: 3
  outliers final: 1
  residues processed: 26
  average time/residue: 0.6604
  time to fit residues: 18.1063
Evaluate side-chains
  27 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue   29 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    0.4980
   chunk 15 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.155564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.133312 restraints weight = 2595.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.54
r_work: 0.3242 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2210  Z= 0.266
  Angle     :  0.643  12.680   3000  Z= 0.320
  Chirality :  0.038   0.139    371
  Planarity :  0.003   0.018    350
  Dihedral  :  8.862  59.683    358
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 22.03 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.51), residues: 260
  helix:  1.48 (0.33), residues: 227
  sheet:  None (None), residues: 0
  loop :  0.52 (1.22), residues: 33

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP B  50 
 HIS   0.002   0.001   HIS A 226 
 PHE   0.025   0.001   PHE A 207 
 TYR   0.016   0.002   TYR B 100 
 ARG   0.001   0.000   ARG B 128 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1721.16 seconds
wall clock time: 31 minutes 39.90 seconds (1899.90 seconds total)