Starting phenix.real_space_refine
on Mon Jan 13 21:51:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h76_51912/01_2025/9h76_51912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h76_51912/01_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_51912/01_2025/9h76_51912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h76_51912/01_2025/9h76_51912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h76_51912/01_2025/9h76_51912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h76_51912/01_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-5571/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: 3.66, per 1000 atoms: 0.88
  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: 1.04
  Conformation dependent library (CDL) restraints added in 536.0 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: 0.49
  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: 1.30

  Time building geometry restraints manager: 1.21 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:             26.340
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     13.000
  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:11.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.000
-------------------------------------------------------------------------------
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  : 0.482 
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: 1.2239
  time to fit residues: 106.5595
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  : 0.498 
-------------------------------------------------------------------------------
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 = 0.3118 r_free = 0.3118 target = 0.085125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.065259 restraints weight = 7448.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.2701 rms_B_bonded: 2.71
r_work: 0.2557 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2557
-------------------------------------------------------------------------------
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: 0.8231
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  : 0.491 
Fit side-chains
REVERT: A    4 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7836 (m)
REVERT: A  213 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8611 (tm-30)
REVERT: A  315 ARG cc_start: 0.7479 (tpp80) cc_final: 0.7048 (ttm170)
REVERT: A  342 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7278 (mt0)
REVERT: B   62 ASP cc_start: 0.8363 (t70) cc_final: 0.7903 (t0)
REVERT: B   88 LYS cc_start: 0.9356 (mttt) cc_final: 0.8917 (mtpp)
REVERT: B   90 GLU cc_start: 0.9235 (pm20) cc_final: 0.8978 (pm20)
REVERT: B   91 ASP cc_start: 0.9339 (m-30) cc_final: 0.8702 (m-30)
REVERT: B  106 GLU cc_start: 0.8692 (tt0) cc_final: 0.8453 (tm-30)
REVERT: B  111 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8591 (pm20)
REVERT: B  114 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8573 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 95
  average time/residue: 1.1064
  time to fit residues: 109.2737
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  : 0.500 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   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 = 0.3118 r_free = 0.3118 target = 0.085226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.065307 restraints weight = 7364.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 2.69
r_work: 0.2562 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2579 r_free = 0.2579    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 = 0.2579 r_free = 0.2579    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1247

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= 0.246
  Angle     :  0.555   6.378   5806  Z= 0.283
  Chirality :  0.042   0.149    698
  Planarity :  0.004   0.044    710
  Dihedral  :  3.759  16.383    586
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 22.32 %
    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:  2.05 (0.37), residues: 542
  helix:  2.10 (0.28), residues: 349
  sheet: -1.17 (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   0.013   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
  99 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8582 (tm-30)
REVERT: A  315 ARG cc_start: 0.7518 (tpp80) cc_final: 0.7162 (ttm110)
REVERT: A  342 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7268 (mt0)
REVERT: B   61 TYR cc_start: 0.9012 (m-80) cc_final: 0.8605 (m-80)
REVERT: B   62 ASP cc_start: 0.8409 (t70) cc_final: 0.7932 (t0)
REVERT: B   74 ASP cc_start: 0.7835 (t0) cc_final: 0.7566 (OUTLIER)
REVERT: B   77 LYS cc_start: 0.9390 (mtpp) cc_final: 0.8932 (ptpp)
REVERT: B   88 LYS cc_start: 0.9346 (mttt) cc_final: 0.8887 (mtpp)
REVERT: B   90 GLU cc_start: 0.9230 (pm20) cc_final: 0.8971 (pm20)
REVERT: B   91 ASP cc_start: 0.9365 (m-30) cc_final: 0.8688 (m-30)
REVERT: B  106 GLU cc_start: 0.8725 (tt0) cc_final: 0.8478 (tm-30)
REVERT: B  111 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8602 (pm20)
  outliers start: 12
  outliers final: 6
  residues processed: 95
  average time/residue: 1.1224
  time to fit residues: 110.6898
Evaluate side-chains
  91 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue  188 THR
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:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 52 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.085511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.065981 restraints weight = 7368.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 2.61
r_work: 0.2619 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2478 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2478
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2498 r_free = 0.2498    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2498 r_free = 0.2498    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4255  Z= 0.230
  Angle     :  0.556   7.233   5806  Z= 0.281
  Chirality :  0.042   0.123    698
  Planarity :  0.004   0.046    710
  Dihedral  :  3.720  14.424    584
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 23.69 %
    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:  1.98 (0.37), residues: 542
  helix:  2.02 (0.28), residues: 350
  sheet: -1.18 (0.63), residues: 56
  loop :  0.76 (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 357 
 TYR   0.007   0.001   TYR A 426 
 ARG   0.012   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
  96 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8647 (tm-30)
REVERT: A  315 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7349 (ttm110)
REVERT: A  342 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7483 (mt0)
REVERT: B   46 GLN cc_start: 0.8469 (pm20) cc_final: 0.8235 (pm20)
REVERT: B   62 ASP cc_start: 0.8538 (t70) cc_final: 0.8021 (t0)
REVERT: B   88 LYS cc_start: 0.9354 (mttt) cc_final: 0.8905 (mttp)
REVERT: B   91 ASP cc_start: 0.9414 (m-30) cc_final: 0.8750 (m-30)
REVERT: B   92 THR cc_start: 0.9108 (t) cc_final: 0.8860 (p)
REVERT: B  106 GLU cc_start: 0.8825 (tt0) cc_final: 0.8603 (tm-30)
REVERT: B  111 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8702 (pm20)
REVERT: B  114 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8687 (tm-30)
  outliers start: 13
  outliers final: 6
  residues processed: 92
  average time/residue: 1.0944
  time to fit residues: 104.6523
Evaluate side-chains
  90 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
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  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  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:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3094 r_free = 0.3094 target = 0.083771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.063701 restraints weight = 7651.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.2713 rms_B_bonded: 2.72
r_work: 0.2570 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2590
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2590 r_free = 0.2590    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 = 0.2590 r_free = 0.2590    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2590
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4255  Z= 0.325
  Angle     :  0.592   7.800   5806  Z= 0.300
  Chirality :  0.043   0.149    698
  Planarity :  0.004   0.047    710
  Dihedral  :  3.775  14.382    584
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 23.92 %
    Favored  : 72.67 %
  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:  1.91 (0.37), residues: 542
  helix:  2.00 (0.28), residues: 350
  sheet: -1.79 (0.64), residues: 47
  loop :  0.71 (0.56), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 355 
 HIS   0.002   0.001   HIS B  81 
 PHE   0.014   0.001   PHE A 357 
 TYR   0.010   0.001   TYR B  96 
 ARG   0.015   0.001   ARG A 296 

*********************** 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
  99 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7158 (tt0)
REVERT: A   75 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8562 (tm-30)
REVERT: A  315 ARG cc_start: 0.7662 (tpp80) cc_final: 0.7296 (ttm110)
REVERT: A  342 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7431 (mt0)
REVERT: B   62 ASP cc_start: 0.8524 (t70) cc_final: 0.8028 (t70)
REVERT: B   88 LYS cc_start: 0.9397 (mttt) cc_final: 0.8931 (mtpp)
REVERT: B   90 GLU cc_start: 0.9261 (pm20) cc_final: 0.9034 (pm20)
REVERT: B   91 ASP cc_start: 0.9470 (m-30) cc_final: 0.8789 (m-30)
REVERT: B   92 THR cc_start: 0.9089 (t) cc_final: 0.8866 (p)
REVERT: B  106 GLU cc_start: 0.8752 (tt0) cc_final: 0.8512 (tt0)
REVERT: B  111 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8618 (pm20)
  outliers start: 15
  outliers final: 10
  residues processed: 94
  average time/residue: 1.1077
  time to fit residues: 108.0675
Evaluate side-chains
  94 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0980
   chunk 26 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3131 r_free = 0.3131 target = 0.085761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.066104 restraints weight = 7353.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 2.64
r_work: 0.2624 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2640
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2640 r_free = 0.2640    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 = 0.2640 r_free = 0.2640    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2640
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4255  Z= 0.213
  Angle     :  0.570   6.445   5806  Z= 0.287
  Chirality :  0.041   0.165    698
  Planarity :  0.005   0.062    710
  Dihedral  :  3.745  14.772    584
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 25.28 %
    Favored  : 71.98 %
  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:  2.04 (0.27), residues: 349
  sheet: -0.75 (0.66), residues: 56
  loop :  0.60 (0.58), 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   0.014   0.001   PHE A 199 
 TYR   0.006   0.001   TYR A  30 
 ARG   0.015   0.001   ARG A 296 

*********************** 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
  99 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7095 (tt0)
REVERT: A   75 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8571 (tm-30)
REVERT: A  315 ARG cc_start: 0.7723 (tpp80) cc_final: 0.7360 (ttm110)
REVERT: A  342 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7528 (mt0)
REVERT: B   21 ARG cc_start: 0.9055 (ptm160) cc_final: 0.8739 (ptm160)
REVERT: B   62 ASP cc_start: 0.8565 (t70) cc_final: 0.8044 (t0)
REVERT: B   74 ASP cc_start: 0.8017 (t0) cc_final: 0.7736 (t0)
REVERT: B   77 LYS cc_start: 0.9418 (mtpp) cc_final: 0.8993 (ptpp)
REVERT: B   88 LYS cc_start: 0.9402 (mttt) cc_final: 0.8917 (mttp)
REVERT: B   91 ASP cc_start: 0.9497 (m-30) cc_final: 0.8834 (m-30)
REVERT: B  111 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8649 (pm20)
REVERT: B  113 THR cc_start: 0.8806 (m) cc_final: 0.8225 (p)
REVERT: B  114 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8606 (tm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 95
  average time/residue: 1.0815
  time to fit residues: 106.7219
Evaluate side-chains
  94 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   32 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0020
   chunk 39 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    0.2980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.085848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.066058 restraints weight = 7414.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.2764 rms_B_bonded: 2.69
r_work: 0.2621 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    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 = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4255  Z= 0.231
  Angle     :  0.598   6.854   5806  Z= 0.300
  Chirality :  0.042   0.168    698
  Planarity :  0.005   0.063    710
  Dihedral  :  3.775  15.399    584
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.83 %
    Favored  : 71.98 %
  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:  2.06 (0.27), residues: 349
  sheet: -0.68 (0.67), residues: 56
  loop :  0.63 (0.59), residues: 137

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 B  96 
 ARG   0.016   0.001   ARG A 296 

*********************** 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
  102 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7068 (tt0)
REVERT: A   75 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8548 (tm-30)
REVERT: A  220 MET cc_start: 0.8162 (tpt) cc_final: 0.7910 (tpp)
REVERT: A  315 ARG cc_start: 0.7725 (tpp80) cc_final: 0.7363 (ttm110)
REVERT: A  342 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7532 (mt0)
REVERT: B   62 ASP cc_start: 0.8555 (t70) cc_final: 0.8040 (t70)
REVERT: B   74 ASP cc_start: 0.8028 (t0) cc_final: 0.7716 (t0)
REVERT: B   77 LYS cc_start: 0.9415 (mtpp) cc_final: 0.9002 (ptpp)
REVERT: B   88 LYS cc_start: 0.9393 (mttt) cc_final: 0.8891 (mttp)
REVERT: B   91 ASP cc_start: 0.9492 (m-30) cc_final: 0.8947 (m-30)
REVERT: B  106 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8320 (tm-30)
REVERT: B  111 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8647 (pm20)
REVERT: B  113 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8358 (p)
REVERT: B  114 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8748 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 95
  average time/residue: 1.0607
  time to fit residues: 104.7825
Evaluate side-chains
  99 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
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    7 VAL
Chi-restraints excluded: chain B residue  106 GLU
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:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3135 r_free = 0.3135 target = 0.086095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.065956 restraints weight = 7356.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 2.74
r_work: 0.2622 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2636 r_free = 0.2636    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 = 0.2636 r_free = 0.2636    target_work(ls_wunit_k1) = 0.058         |
| 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: 0.8391
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4255  Z= 0.246
  Angle     :  0.606   6.691   5806  Z= 0.305
  Chirality :  0.042   0.169    698
  Planarity :  0.005   0.064    710
  Dihedral  :  3.788  15.765    584
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.83 %
    Favored  : 71.98 %
  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:  2.07 (0.27), residues: 349
  sheet: -1.31 (0.71), residues: 47
  loop :  0.63 (0.55), residues: 146

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 357 
 TYR   0.007   0.001   TYR B  61 
 ARG   0.018   0.002   ARG A 296 

*********************** 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
  101 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7041 (tt0)
REVERT: A   75 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8544 (tm-30)
REVERT: A  220 MET cc_start: 0.8123 (tpt) cc_final: 0.7873 (tpp)
REVERT: A  315 ARG cc_start: 0.7672 (tpp80) cc_final: 0.7305 (ttm110)
REVERT: A  342 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7471 (mt0)
REVERT: B   21 ARG cc_start: 0.9061 (ptm160) cc_final: 0.8828 (ptm160)
REVERT: B   62 ASP cc_start: 0.8522 (t70) cc_final: 0.7995 (t70)
REVERT: B   74 ASP cc_start: 0.8017 (t0) cc_final: 0.7681 (t0)
REVERT: B   77 LYS cc_start: 0.9406 (mtpp) cc_final: 0.8997 (ptpp)
REVERT: B   88 LYS cc_start: 0.9413 (mttt) cc_final: 0.8842 (mtmm)
REVERT: B   91 ASP cc_start: 0.9498 (m-30) cc_final: 0.8947 (m-30)
REVERT: B  106 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8323 (tm-30)
REVERT: B  111 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8622 (pm20)
REVERT: B  113 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8298 (p)
REVERT: B  114 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8716 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 93
  average time/residue: 1.0989
  time to fit residues: 106.1531
Evaluate side-chains
  99 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
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    7 VAL
Chi-restraints excluded: chain B residue  106 GLU
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:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0010
   chunk 4 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0970
   overall best weight:    0.3784

-------------------------------------------------------------------------------
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 = 0.3166 r_free = 0.3166 target = 0.087940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.068082 restraints weight = 7366.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 2.71
r_work: 0.2656 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    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 = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4255  Z= 0.207
  Angle     :  0.606   7.552   5806  Z= 0.304
  Chirality :  0.042   0.173    698
  Planarity :  0.005   0.073    710
  Dihedral  :  3.780  15.603    584
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 25.97 %
    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:  2.06 (0.37), residues: 542
  helix:  2.11 (0.27), residues: 349
  sheet: -0.88 (0.70), residues: 53
  loop :  0.54 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.013   0.001   PHE A 199 
 TYR   0.015   0.001   TYR B  96 
 ARG   0.019   0.002   ARG A 296 

*********************** 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
  104 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8550 (tm-30)
REVERT: A  220 MET cc_start: 0.8144 (tpt) cc_final: 0.7880 (tpp)
REVERT: A  315 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7343 (ttm110)
REVERT: A  342 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7507 (mt0)
REVERT: A  372 GLN cc_start: 0.8822 (mt0) cc_final: 0.8560 (pt0)
REVERT: B   62 ASP cc_start: 0.8515 (t70) cc_final: 0.7976 (t70)
REVERT: B   74 ASP cc_start: 0.8059 (t0) cc_final: 0.7751 (t0)
REVERT: B   77 LYS cc_start: 0.9410 (mtpp) cc_final: 0.9042 (ptpp)
REVERT: B   91 ASP cc_start: 0.9476 (m-30) cc_final: 0.9047 (m-30)
REVERT: B  106 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8285 (tm-30)
REVERT: B  111 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8649 (pm20)
REVERT: B  113 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8440 (p)
  outliers start: 12
  outliers final: 6
  residues processed: 97
  average time/residue: 1.1559
  time to fit residues: 116.6383
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  : 0.485 
-------------------------------------------------------------------------------
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  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue  106 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 30 optimal weight:    0.0670
   chunk 1 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.3147 r_free = 0.3147 target = 0.086459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.066671 restraints weight = 7382.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 2.70
r_work: 0.2631 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    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 = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2654
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4255  Z= 0.244
  Angle     :  0.620   7.395   5806  Z= 0.311
  Chirality :  0.042   0.176    698
  Planarity :  0.004   0.046    710
  Dihedral  :  3.806  16.286    584
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 26.42 %
    Favored  : 71.07 %
  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:  2.10 (0.27), residues: 349
  sheet: -0.84 (0.70), residues: 53
  loop :  0.68 (0.57), 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   0.013   0.001   PHE A 199 
 TYR   0.007   0.001   TYR A  95 
 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
  100 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8559 (tm-30)
REVERT: A  220 MET cc_start: 0.8162 (tpt) cc_final: 0.7962 (tpp)
REVERT: A  296 ARG cc_start: 0.8437 (ttm110) cc_final: 0.8052 (mtt90)
REVERT: A  315 ARG cc_start: 0.7713 (tpp80) cc_final: 0.7350 (ttm110)
REVERT: A  342 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7514 (mt0)
REVERT: A  372 GLN cc_start: 0.8809 (mt0) cc_final: 0.8505 (pt0)
REVERT: B   62 ASP cc_start: 0.8509 (t70) cc_final: 0.7985 (t70)
REVERT: B   74 ASP cc_start: 0.8062 (t0) cc_final: 0.7753 (t0)
REVERT: B   77 LYS cc_start: 0.9412 (mtpp) cc_final: 0.9043 (ptpp)
REVERT: B   91 ASP cc_start: 0.9473 (m-30) cc_final: 0.8995 (m-30)
REVERT: B  106 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8323 (tm-30)
REVERT: B  111 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8650 (pm20)
REVERT: B  113 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8375 (p)
  outliers start: 11
  outliers final: 6
  residues processed: 92
  average time/residue: 1.0921
  time to fit residues: 104.6507
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  : 0.448 
-------------------------------------------------------------------------------
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  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue  106 GLU
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=1.00
-------------------------------------------------------------------------------
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:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 42 optimal weight:    0.2980
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0970
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3161 r_free = 0.3161 target = 0.086933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.066672 restraints weight = 7356.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.2787 rms_B_bonded: 2.75
r_work: 0.2646 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2664 r_free = 0.2664    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 = 0.2664 r_free = 0.2664    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2032

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= 0.222
  Angle     :  0.614   7.899   5806  Z= 0.308
  Chirality :  0.042   0.174    698
  Planarity :  0.004   0.046    710
  Dihedral  :  3.803  16.770    584
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 27.11 %
    Favored  : 70.84 %
  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 (0.37), residues: 542
  helix:  2.12 (0.27), residues: 349
  sheet: -1.23 (0.72), residues: 47
  loop :  0.82 (0.56), residues: 146

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   0.013   0.001   TYR B  96 
 ARG   0.011   0.001   ARG B  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3518.14 seconds
wall clock time: 63 minutes 45.13 seconds (3825.13 seconds total)