Starting phenix.real_space_refine
on Thu Mar  6 00:34:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h76_51912/03_2025/9h76_51912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h76_51912/03_2025/9h76_51912.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h76_51912/03_2025/9h76_51912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h76_51912/03_2025/9h76_51912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h76_51912/03_2025/9h76_51912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h76_51912/03_2025/9h76_51912.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2756      2.51       5
     N     661      2.21       5
     O     724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4157
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3263
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 406}
    Chain: "B"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 888
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 2, 'TRANS': 113}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   LYS A 154 " occ=0.82
      ... (7 atoms not shown)
      pdb=" NZ  LYS A 154 " occ=0.82
    residue:
      pdb=" N   ALA A 501 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OXT ALA A 501 " occ=0.00
  Time building chain proxies: 5.12, per 1000 atoms: 1.23
  Number of scatterers: 4157
  At special positions: 0
  Unit cell: (72.93, 75.99, 99.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     724      8.00
     N     661      7.00
     C    2756      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " 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: 1.05
  Conformation dependent library (CDL) restraints added in 518.7 milliseconds
  

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  976

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 4 sheets defined
      71.1% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 18
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.728A  pdb=" N   PHE A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 33
    Processing helix  chain 'A' and resid 35 through 64
      removed outlier: 3.556A  pdb=" N   LEU A  40 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE A  60 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 78
    Processing helix  chain 'A' and resid 79 through 93
    Processing helix  chain 'A' and resid 93 through 115
    Processing helix  chain 'A' and resid 117 through 119
      No H-bonds generated for 'chain 'A' and resid 117 through 119'
    Processing helix  chain 'A' and resid 120 through 137
    Processing helix  chain 'A' and resid 139 through 154
      removed outlier: 4.248A  pdb=" N   SER A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 167
      removed outlier: 3.986A  pdb=" N   LEU A 158 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 177
      removed outlier: 3.623A  pdb=" N   VAL A 177 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 201
      removed outlier: 4.029A  pdb=" N   GLY A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA A 200 " --> pdb=" O   ALA A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 205 through 214
      removed outlier: 4.174A  pdb=" N   THR A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLY A 212 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU A 213 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 247
      removed outlier: 4.310A  pdb=" N   LYS A 223 " --> pdb=" O   LYS A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 254
    Processing helix  chain 'A' and resid 257 through 267
    Processing helix  chain 'A' and resid 269 through 304
      removed outlier: 4.351A  pdb=" N   LYS A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
      Proline residue:  A 298  - end of helix
      removed outlier: 3.612A  pdb=" N   GLN A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 315
    Processing helix  chain 'A' and resid 324 through 340
    Processing helix  chain 'A' and resid 342 through 372
    Processing helix  chain 'A' and resid 386 through 406
    Processing helix  chain 'A' and resid 406 through 431
      Proline residue:  A 422  - end of helix
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'B' and resid 88 through 92
    Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 8
      removed outlier: 3.567A  pdb=" N   LEU B  20 " --> pdb=" O   MET B  84 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 8
      removed outlier: 3.534A  pdb=" N   THR B  79 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 14
      removed outlier: 3.662A  pdb=" N   VAL B  94 " --> pdb=" O   GLN B  41 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   MET B  36 " --> pdb=" O   ARG B  52 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ARG B  52 " --> pdb=" O   MET B  36 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   TRP B  38 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14

    310 hydrogen bonds defined for protein.
    879 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: 1.25

  Time building geometry restraints manager: 1.27 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: 671
        1.33 -     1.45: 1119
        1.45 -     1.57: 2436
        1.57 -     1.69: 0
        1.69 -     1.81: 29
  Bond restraints: 4255
  Sorted by residual:
  bond pdb=" CB  MET B  84 "
       pdb=" CG  MET B  84 "
    ideal  model  delta    sigma   weight residual
    1.520  1.457  0.063 3.00e-02 1.11e+03 4.47e+00
  bond pdb=" SD  MET A 233 "
       pdb=" CE  MET A 233 "
    ideal  model  delta    sigma   weight residual
    1.791  1.748  0.043 2.50e-02 1.60e+03 3.01e+00
  bond pdb=" CA  GLN B  15 "
       pdb=" C   GLN B  15 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.019 1.30e-02 5.92e+03 2.07e+00
  bond pdb=" CD  GLN B  15 "
       pdb=" OE1 GLN B  15 "
    ideal  model  delta    sigma   weight residual
    1.231  1.205  0.026 1.90e-02 2.77e+03 1.82e+00
  bond pdb=" N   GLY A  19 "
       pdb=" CA  GLY A  19 "
    ideal  model  delta    sigma   weight residual
    1.458  1.446  0.012 9.20e-03 1.18e+04 1.59e+00
  ... (remaining 4250 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 5540
        1.13 -     2.26: 186
        2.26 -     3.40: 52
        3.40 -     4.53: 17
        4.53 -     5.66: 11
  Bond angle restraints: 5806
  Sorted by residual:
  angle pdb=" CB  GLU A  75 "
        pdb=" CG  GLU A  75 "
        pdb=" CD  GLU A  75 "
      ideal   model   delta    sigma   weight residual
     112.60  118.26   -5.66 1.70e+00 3.46e-01 1.11e+01
  angle pdb=" CA  GLU A  75 "
        pdb=" CB  GLU A  75 "
        pdb=" CG  GLU A  75 "
      ideal   model   delta    sigma   weight residual
     114.10  119.32   -5.22 2.00e+00 2.50e-01 6.82e+00
  angle pdb=" CB  GLN B   5 "
        pdb=" CG  GLN B   5 "
        pdb=" CD  GLN B   5 "
      ideal   model   delta    sigma   weight residual
     112.60  116.66   -4.06 1.70e+00 3.46e-01 5.71e+00
  angle pdb=" CB  GLU A 376 "
        pdb=" CG  GLU A 376 "
        pdb=" CD  GLU A 376 "
      ideal   model   delta    sigma   weight residual
     112.60  116.52   -3.92 1.70e+00 3.46e-01 5.32e+00
  angle pdb=" CA  GLN B  15 "
        pdb=" CB  GLN B  15 "
        pdb=" CG  GLN B  15 "
      ideal   model   delta    sigma   weight residual
     114.10  118.56   -4.46 2.00e+00 2.50e-01 4.98e+00
  ... (remaining 5801 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 2141
       17.55 -    35.10: 241
       35.10 -    52.64: 61
       52.64 -    70.19: 7
       70.19 -    87.74: 4
  Dihedral angle restraints: 2454
    sinusoidal: 909
      harmonic: 1545
  Sorted by residual:
  dihedral pdb=" N   ASN B 107 "
           pdb=" CA  ASN B 107 "
           pdb=" CB  ASN B 107 "
           pdb=" CG  ASN B 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.54  -59.46     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS A  76 "
           pdb=" CD  LYS A  76 "
           pdb=" CE  LYS A  76 "
           pdb=" NZ  LYS A  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.33   59.33     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LYS B  66 "
           pdb=" CB  LYS B  66 "
           pdb=" CG  LYS B  66 "
           pdb=" CD  LYS B  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.79  -57.79     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 2451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 397
       0.028 -    0.056: 179
       0.056 -    0.084: 77
       0.084 -    0.112: 38
       0.112 -    0.140: 7
  Chirality restraints: 698
  Sorted by residual:
  chirality pdb=" CA  VAL B   4 "
            pdb=" N   VAL B   4 "
            pdb=" C   VAL B   4 "
            pdb=" CB  VAL B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CB  VAL B   4 "
            pdb=" CA  VAL B   4 "
            pdb=" CG1 VAL B   4 "
            pdb=" CG2 VAL B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  VAL B 102 "
            pdb=" N   VAL B 102 "
            pdb=" C   VAL B 102 "
            pdb=" CB  VAL B 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.32e-01
  ... (remaining 695 not shown)

  Planarity restraints: 710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 296 "   -0.174 9.50e-02 1.11e+02   7.84e-02 4.76e+00
        pdb=" NE  ARG A 296 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 296 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 296 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 296 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 387 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.66e+00
        pdb=" N   PRO A 388 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 388 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 388 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 122 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.90e+00
        pdb=" N   PRO A 123 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 123 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 123 "    0.020 5.00e-02 4.00e+02
  ... (remaining 707 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 30
        2.62 -     3.19: 3992
        3.19 -     3.76: 6720
        3.76 -     4.33: 9200
        4.33 -     4.90: 15696
  Nonbonded interactions: 35638
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B  15 "
            pdb=" N   ALA B  16 "
     model   vdw
     2.053 3.120
  nonbonded pdb=" N   GLU B  90 "
            pdb=" OE1 GLU B  90 "
     model   vdw
     2.135 3.120
  nonbonded pdb=" OE2 GLU A  59 "
            pdb=" NH2 ARG A 369 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" N   GLN B  46 "
            pdb=" OE1 GLN B  46 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   PHE B  31 "
            pdb=" NH2 ARG B  73 "
     model   vdw
     2.266 3.120
  ... (remaining 35633 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             12.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.760
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:12.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
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      :  0.005   0.063   4255  Z= 0.297
  Angle     :  0.593   5.660   5806  Z= 0.302
  Chirality :  0.042   0.140    698
  Planarity :  0.005   0.078    710
  Dihedral  : 15.748  87.739   1475
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 25.28 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 (0.38), residues: 542
  helix:  2.34 (0.29), residues: 346
  sheet: -2.18 (0.75), residues: 41
  loop :  0.45 (0.52), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.014   0.001   PHE A 357 
 TYR   0.010   0.001   TYR A 424 
 ARG   0.018   0.001   ARG A 296 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8823 (tm-30)
REVERT: A  315 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7649 (ttm170)
REVERT: B   61 TYR cc_start: 0.9265 (m-80) cc_final: 0.8896 (m-80)
REVERT: B   62 ASP cc_start: 0.8660 (t70) cc_final: 0.8153 (t0)
REVERT: B   88 LYS cc_start: 0.9576 (mttt) cc_final: 0.9083 (mtpp)
REVERT: B   90 GLU cc_start: 0.9064 (pm20) cc_final: 0.8773 (pm20)
REVERT: B   91 ASP cc_start: 0.9508 (m-30) cc_final: 0.8920 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 84
  average time/residue: 1.1956
  time to fit residues: 104.0577
Evaluate side-chains
  82 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0970
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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 = 0.3117 r_free = 0.3117 target = 0.085046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.065178 restraints weight = 7438.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.2703 rms_B_bonded: 2.70
r_work: 0.2559 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.0996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4255  Z= 0.253
  Angle     :  0.556   7.390   5806  Z= 0.287
  Chirality :  0.042   0.129    698
  Planarity :  0.005   0.044    710
  Dihedral  :  3.732  16.786    586
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.18 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.08 (0.37), residues: 542
  helix:  2.17 (0.28), residues: 350
  sheet: -2.00 (0.70), residues: 44
  loop :  0.72 (0.54), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.016   0.001   PHE A 357 
 TYR   0.009   0.001   TYR A 426 
 ARG   0.009   0.001   ARG A 296 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A    4 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7832 (m)
REVERT: A  213 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8610 (tm-30)
REVERT: A  315 ARG cc_start: 0.7474 (tpp80) cc_final: 0.7042 (ttm170)
REVERT: A  342 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7269 (mt0)
REVERT: B   62 ASP cc_start: 0.8358 (t70) cc_final: 0.7898 (t0)
REVERT: B   88 LYS cc_start: 0.9355 (mttt) cc_final: 0.8916 (mtpp)
REVERT: B   90 GLU cc_start: 0.9235 (pm20) cc_final: 0.8977 (pm20)
REVERT: B   91 ASP cc_start: 0.9338 (m-30) cc_final: 0.8701 (m-30)
REVERT: B  106 GLU cc_start: 0.8691 (tt0) cc_final: 0.8452 (tm-30)
REVERT: B  111 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8589 (pm20)
REVERT: B  114 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8572 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 95
  average time/residue: 1.0450
  time to fit residues: 103.3142
Evaluate side-chains
  92 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.085273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.065349 restraints weight = 7370.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.2704 rms_B_bonded: 2.70
r_work: 0.2559 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4255  Z= 0.247
  Angle     :  0.555   6.363   5806  Z= 0.283
  Chirality :  0.042   0.145    698
  Planarity :  0.004   0.044    710
  Dihedral  :  3.753  16.673    586
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.55 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.06 (0.37), residues: 542
  helix:  2.11 (0.28), residues: 349
  sheet: -1.16 (0.65), residues: 53
  loop :  0.66 (0.58), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.014   0.001   PHE A 357 
 TYR   0.012   0.001   TYR B  96 
 ARG   0.011   0.001   ARG A 296 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 1.251 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8603 (tm-30)
REVERT: A  315 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7208 (ttm110)
REVERT: A  342 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7335 (mt0)
REVERT: B   61 TYR cc_start: 0.9038 (m-80) cc_final: 0.8641 (m-80)
REVERT: B   62 ASP cc_start: 0.8444 (t70) cc_final: 0.7945 (t0)
REVERT: B   74 ASP cc_start: 0.7884 (t0) cc_final: 0.7623 (OUTLIER)
REVERT: B   77 LYS cc_start: 0.9396 (mtpp) cc_final: 0.8939 (ptpp)
REVERT: B   88 LYS cc_start: 0.9367 (mttt) cc_final: 0.8899 (mtpp)
REVERT: B   90 GLU cc_start: 0.9232 (pm20) cc_final: 0.8984 (pm20)
REVERT: B   91 ASP cc_start: 0.9389 (m-30) cc_final: 0.8714 (m-30)
REVERT: B  106 GLU cc_start: 0.8732 (tt0) cc_final: 0.8492 (tm-30)
REVERT: B  111 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8615 (pm20)
  outliers start: 11
  outliers final: 5
  residues processed: 94
  average time/residue: 1.1775
  time to fit residues: 115.4943
Evaluate side-chains
  91 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0170
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0010
   chunk 45 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.4424

-------------------------------------------------------------------------------
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 = 0.3137 r_free = 0.3137 target = 0.086265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.066541 restraints weight = 7345.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 2.65
r_work: 0.2629 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4255  Z= 0.200
  Angle     :  0.549   6.813   5806  Z= 0.278
  Chirality :  0.041   0.123    698
  Planarity :  0.004   0.046    710
  Dihedral  :  3.686  14.546    584
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.92 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.07 (0.37), residues: 542
  helix:  2.09 (0.28), residues: 350
  sheet: -1.13 (0.64), residues: 56
  loop :  0.77 (0.59), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.013   0.001   PHE A 199 
 TYR   0.007   0.001   TYR A 426 
 ARG   0.014   0.001   ARG A 296 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A  315 ARG cc_start: 0.7681 (tpp80) cc_final: 0.7313 (ttm110)
REVERT: A  342 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7454 (mt0)
REVERT: B   61 TYR cc_start: 0.9100 (m-80) cc_final: 0.8689 (m-80)
REVERT: B   62 ASP cc_start: 0.8511 (t70) cc_final: 0.8014 (t0)
REVERT: B   88 LYS cc_start: 0.9397 (mttt) cc_final: 0.8957 (mttp)
REVERT: B   91 ASP cc_start: 0.9439 (m-30) cc_final: 0.8824 (m-30)
REVERT: B   92 THR cc_start: 0.9098 (t) cc_final: 0.8857 (p)
REVERT: B  106 GLU cc_start: 0.8736 (tt0) cc_final: 0.8471 (tm-30)
REVERT: B  111 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8631 (pm20)
REVERT: B  113 THR cc_start: 0.8747 (m) cc_final: 0.8167 (p)
  outliers start: 12
  outliers final: 5
  residues processed: 92
  average time/residue: 1.1137
  time to fit residues: 106.4552
Evaluate side-chains
  88 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3111 r_free = 0.3111 target = 0.084775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.064675 restraints weight = 7610.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2731 rms_B_bonded: 2.72
r_work: 0.2586 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2605
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2605 r_free = 0.2605    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2605 r_free = 0.2605    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2605
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4255  Z= 0.283
  Angle     :  0.580   7.357   5806  Z= 0.294
  Chirality :  0.043   0.149    698
  Planarity :  0.004   0.047    710
  Dihedral  :  3.728  14.830    584
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.60 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 (0.37), residues: 542
  helix:  2.08 (0.28), residues: 349
  sheet: -0.73 (0.62), residues: 63
  loop :  0.58 (0.61), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.014   0.001   PHE A 357 
 TYR   0.010   0.001   TYR B  96 
 ARG   0.006   0.001   ARG B  21 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A  315 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7322 (ttm110)
REVERT: A  342 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7484 (mt0)
REVERT: B   62 ASP cc_start: 0.8524 (t70) cc_final: 0.8006 (t70)
REVERT: B   88 LYS cc_start: 0.9411 (mttt) cc_final: 0.8952 (mtpp)
REVERT: B   90 GLU cc_start: 0.9271 (pm20) cc_final: 0.9050 (pm20)
REVERT: B   91 ASP cc_start: 0.9470 (m-30) cc_final: 0.8760 (m-30)
REVERT: B   92 THR cc_start: 0.9086 (t) cc_final: 0.8874 (p)
REVERT: B  111 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8626 (pm20)
  outliers start: 14
  outliers final: 10
  residues processed: 93
  average time/residue: 1.1005
  time to fit residues: 106.4237
Evaluate side-chains
  94 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   32 SER
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0060
   chunk 26 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.3132 r_free = 0.3132 target = 0.086035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.066346 restraints weight = 7394.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.2764 rms_B_bonded: 2.68
r_work: 0.2621 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2636 r_free = 0.2636    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2636 r_free = 0.2636    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2636
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4255  Z= 0.222
  Angle     :  0.563   6.466   5806  Z= 0.286
  Chirality :  0.041   0.127    698
  Planarity :  0.004   0.047    710
  Dihedral  :  3.742  15.196    584
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 24.37 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.07 (0.37), residues: 542
  helix:  2.10 (0.27), residues: 349
  sheet: -0.55 (0.63), residues: 63
  loop :  0.53 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.013   0.001   PHE A 199 
 TYR   0.026   0.001   TYR B  96 
 ARG   0.012   0.001   ARG B  21 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7079 (tt0)
REVERT: A  296 ARG cc_start: 0.8472 (ttm170) cc_final: 0.8118 (mtt90)
REVERT: A  315 ARG cc_start: 0.7724 (tpp80) cc_final: 0.7362 (ttm110)
REVERT: A  342 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7527 (mt0)
REVERT: B   21 ARG cc_start: 0.9057 (ptm160) cc_final: 0.8766 (ptm160)
REVERT: B   61 TYR cc_start: 0.9121 (m-80) cc_final: 0.8685 (m-80)
REVERT: B   62 ASP cc_start: 0.8559 (t70) cc_final: 0.8049 (t70)
REVERT: B   74 ASP cc_start: 0.7998 (t0) cc_final: 0.7715 (t0)
REVERT: B   77 LYS cc_start: 0.9417 (mtpp) cc_final: 0.8992 (ptpp)
REVERT: B   88 LYS cc_start: 0.9406 (mttt) cc_final: 0.8918 (mttp)
REVERT: B   91 ASP cc_start: 0.9476 (m-30) cc_final: 0.8828 (m-30)
REVERT: B   92 THR cc_start: 0.9105 (t) cc_final: 0.8889 (p)
REVERT: B  113 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8281 (p)
  outliers start: 15
  outliers final: 10
  residues processed: 95
  average time/residue: 1.0934
  time to fit residues: 107.8815
Evaluate side-chains
  95 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   32 SER
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0010
   chunk 39 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.7190

-------------------------------------------------------------------------------
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 = 0.3125 r_free = 0.3125 target = 0.085481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.065823 restraints weight = 7479.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.2748 rms_B_bonded: 2.67
r_work: 0.2605 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2627 r_free = 0.2627    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2627 r_free = 0.2627    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4255  Z= 0.261
  Angle     :  0.600   7.296   5806  Z= 0.303
  Chirality :  0.042   0.154    698
  Planarity :  0.004   0.047    710
  Dihedral  :  3.783  15.442    584
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 24.37 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.02 (0.37), residues: 542
  helix:  2.03 (0.27), residues: 349
  sheet: -0.45 (0.65), residues: 63
  loop :  0.54 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.013   0.001   PHE A 357 
 TYR   0.007   0.001   TYR A  30 
 ARG   0.010   0.001   ARG B  21 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7087 (tt0)
REVERT: A  220 MET cc_start: 0.8173 (tpt) cc_final: 0.7912 (tpp)
REVERT: A  296 ARG cc_start: 0.8485 (ttm170) cc_final: 0.8154 (mtt90)
REVERT: A  315 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7355 (ttm110)
REVERT: A  342 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7539 (mt0)
REVERT: A  372 GLN cc_start: 0.8851 (mt0) cc_final: 0.8581 (pt0)
REVERT: B   62 ASP cc_start: 0.8562 (t70) cc_final: 0.8049 (t70)
REVERT: B   74 ASP cc_start: 0.8020 (t0) cc_final: 0.7696 (t0)
REVERT: B   77 LYS cc_start: 0.9416 (mtpp) cc_final: 0.8998 (ptpp)
REVERT: B   88 LYS cc_start: 0.9404 (mttt) cc_final: 0.8932 (mtpp)
REVERT: B   91 ASP cc_start: 0.9482 (m-30) cc_final: 0.8840 (m-30)
REVERT: B  106 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8327 (tm-30)
REVERT: B  111 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8637 (pm20)
  outliers start: 15
  outliers final: 11
  residues processed: 92
  average time/residue: 1.0670
  time to fit residues: 102.0545
Evaluate side-chains
  95 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.4980
   chunk 53 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   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 = 0.3149 r_free = 0.3149 target = 0.086934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.067309 restraints weight = 7346.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 2.68
r_work: 0.2633 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2655 r_free = 0.2655    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2655 r_free = 0.2655    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4255  Z= 0.216
  Angle     :  0.596   6.817   5806  Z= 0.302
  Chirality :  0.042   0.172    698
  Planarity :  0.004   0.047    710
  Dihedral  :  3.783  15.535    584
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.60 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.12 (0.37), residues: 542
  helix:  2.10 (0.27), residues: 349
  sheet: -0.58 (0.69), residues: 56
  loop :  0.64 (0.59), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.013   0.001   PHE A 199 
 TYR   0.018   0.001   TYR B  96 
 ARG   0.015   0.001   ARG B  21 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7006 (tt0)
REVERT: A  220 MET cc_start: 0.8135 (tpt) cc_final: 0.7892 (tpp)
REVERT: A  296 ARG cc_start: 0.8458 (ttm170) cc_final: 0.8122 (mtt90)
REVERT: A  315 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7346 (ttm110)
REVERT: A  342 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7510 (mt0)
REVERT: A  372 GLN cc_start: 0.8813 (mt0) cc_final: 0.8575 (pt0)
REVERT: B   21 ARG cc_start: 0.9077 (ptm160) cc_final: 0.8843 (ptm160)
REVERT: B   62 ASP cc_start: 0.8544 (t70) cc_final: 0.8014 (t70)
REVERT: B   74 ASP cc_start: 0.8019 (t0) cc_final: 0.7685 (t0)
REVERT: B   77 LYS cc_start: 0.9410 (mtpp) cc_final: 0.9015 (ptpp)
REVERT: B   88 LYS cc_start: 0.9395 (mttt) cc_final: 0.8795 (mttm)
REVERT: B   91 ASP cc_start: 0.9477 (m-30) cc_final: 0.8918 (m-30)
REVERT: B  106 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8293 (tm-30)
REVERT: B  111 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8628 (pm20)
REVERT: B  113 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8342 (p)
  outliers start: 13
  outliers final: 9
  residues processed: 98
  average time/residue: 1.3829
  time to fit residues: 140.8044
Evaluate side-chains
  100 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 30 optimal weight:    0.2980
   chunk 12 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0980
   chunk 18 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   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 = 0.3153 r_free = 0.3153 target = 0.087156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.067541 restraints weight = 7421.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 2.69
r_work: 0.2644 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4255  Z= 0.216
  Angle     :  0.600   7.269   5806  Z= 0.301
  Chirality :  0.042   0.169    698
  Planarity :  0.004   0.048    710
  Dihedral  :  3.772  16.220    584
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 26.20 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.11 (0.37), residues: 542
  helix:  2.12 (0.27), residues: 349
  sheet: -0.82 (0.70), residues: 53
  loop :  0.63 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 355 
 HIS   0.002   0.001   HIS B  81 
 PHE   0.014   0.001   PHE A 199 
 TYR   0.006   0.001   TYR A  95 
 ARG   0.013   0.001   ARG B  21 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8501 (tm-30)
REVERT: A  220 MET cc_start: 0.8139 (tpt) cc_final: 0.7852 (tpp)
REVERT: A  296 ARG cc_start: 0.8472 (ttm170) cc_final: 0.8139 (mtt90)
REVERT: A  315 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7347 (ttm110)
REVERT: A  342 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7519 (mt0)
REVERT: A  372 GLN cc_start: 0.8777 (mt0) cc_final: 0.8525 (pt0)
REVERT: B   62 ASP cc_start: 0.8536 (t70) cc_final: 0.7985 (t70)
REVERT: B   74 ASP cc_start: 0.8041 (t0) cc_final: 0.7742 (t0)
REVERT: B   77 LYS cc_start: 0.9411 (mtpp) cc_final: 0.9047 (ptpp)
REVERT: B   88 LYS cc_start: 0.9454 (mttt) cc_final: 0.8959 (mttp)
REVERT: B   91 ASP cc_start: 0.9468 (m-30) cc_final: 0.8901 (m-30)
REVERT: B  106 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8306 (tm-30)
REVERT: B  113 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8343 (p)
  outliers start: 11
  outliers final: 6
  residues processed: 96
  average time/residue: 1.7367
  time to fit residues: 173.0212
Evaluate side-chains
  98 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 30 optimal weight:    0.4980
   chunk 1 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3158 r_free = 0.3158 target = 0.087384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.067584 restraints weight = 7364.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.72
r_work: 0.2641 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4255  Z= 0.226
  Angle     :  0.605   7.766   5806  Z= 0.304
  Chirality :  0.042   0.173    698
  Planarity :  0.004   0.047    710
  Dihedral  :  3.802  16.577    584
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 26.42 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.13 (0.37), residues: 542
  helix:  2.13 (0.27), residues: 349
  sheet: -0.76 (0.71), residues: 53
  loop :  0.61 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.013   0.001   PHE A 199 
 TYR   0.008   0.001   TYR B  96 
 ARG   0.012   0.001   ARG B  21 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8507 (tm-30)
REVERT: A  220 MET cc_start: 0.8131 (tpt) cc_final: 0.7851 (tpp)
REVERT: A  296 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8142 (mtt90)
REVERT: A  315 ARG cc_start: 0.7719 (tpp80) cc_final: 0.7358 (ttm110)
REVERT: A  342 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7516 (mt0)
REVERT: A  372 GLN cc_start: 0.8776 (mt0) cc_final: 0.8549 (pt0)
REVERT: B   62 ASP cc_start: 0.8517 (t70) cc_final: 0.7965 (t70)
REVERT: B   74 ASP cc_start: 0.8040 (t0) cc_final: 0.7746 (t0)
REVERT: B   77 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9059 (ptpp)
REVERT: B   88 LYS cc_start: 0.9421 (mttt) cc_final: 0.8893 (mttp)
REVERT: B   91 ASP cc_start: 0.9449 (m-30) cc_final: 0.8958 (m-30)
REVERT: B  106 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8363 (tm-30)
REVERT: B  113 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8362 (p)
  outliers start: 9
  outliers final: 8
  residues processed: 93
  average time/residue: 1.0457
  time to fit residues: 101.2154
Evaluate side-chains
  98 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 7 optimal weight:    0.3980
   chunk 45 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 27 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 = 0.3143 r_free = 0.3143 target = 0.086441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.066589 restraints weight = 7383.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.2769 rms_B_bonded: 2.71
r_work: 0.2633 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4255  Z= 0.253
  Angle     :  0.615   7.717   5806  Z= 0.308
  Chirality :  0.042   0.177    698
  Planarity :  0.004   0.047    710
  Dihedral  :  3.821  17.372    584
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 26.20 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.08 (0.37), residues: 542
  helix:  2.11 (0.27), residues: 349
  sheet: -0.88 (0.69), residues: 53
  loop :  0.60 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 355 
 HIS   0.002   0.001   HIS B  81 
 PHE   0.013   0.001   PHE A 199 
 TYR   0.007   0.001   TYR B  60 
 ARG   0.012   0.001   ARG B  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3799.84 seconds
wall clock time: 67 minutes 8.81 seconds (4028.81 seconds total)