Starting phenix.real_space_refine
on Sun Apr 27 01:08:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s5w_19752/04_2025/8s5w_19752.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s5w_19752/04_2025/8s5w_19752.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s5w_19752/04_2025/8s5w_19752.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s5w_19752/04_2025/8s5w_19752.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s5w_19752/04_2025/8s5w_19752.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s5w_19752/04_2025/8s5w_19752.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.053
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      21      5.16       5
     C    2662      2.51       5
     N     626      2.21       5
     O     700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4009
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 935
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 3037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3037
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 13, 'TRANS': 366}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'2TA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.62, per 1000 atoms: 0.90
  Number of scatterers: 4009
  At special positions: 0
  Unit cell: (100.43, 79.68, 77.19, 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      21     16.00
     O     700      8.00
     N     626      7.00
     C    2662      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 440.3 milliseconds
  

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  936

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 4 sheets defined
      61.8% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 28
      removed outlier: 3.651A  pdb=" N   THR A  16 " --> pdb=" O   TRP A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 40
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 56 through 66
      removed outlier: 4.383A  pdb=" N   THR A  60 " --> pdb=" O   PHE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 77
      removed outlier: 3.600A  pdb=" N   ASP A  75 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 99
      removed outlier: 4.204A  pdb=" N   VAL A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 119
      removed outlier: 3.622A  pdb=" N   MET A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 129
      removed outlier: 3.745A  pdb=" N   TYR A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ILE A 127 " --> pdb=" O   TYR A 123 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   TYR A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   SER A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 163
      removed outlier: 3.707A  pdb=" N   THR A 147 " --> pdb=" O   CYS A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 187
      removed outlier: 3.647A  pdb=" N   ASN A 173 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ILE A 175 " --> pdb=" O   TYR A 171 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   PHE A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 274
      removed outlier: 3.655A  pdb=" N   SER A 274 " --> pdb=" O   GLU A 271 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 271 through 274'
    Processing helix  chain 'A' and resid 275 through 298
      removed outlier: 3.539A  pdb=" N   TRP A 284 " --> pdb=" O   TYR A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 307
    Processing helix  chain 'A' and resid 315 through 337
      removed outlier: 3.601A  pdb=" N   GLY A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 366
      removed outlier: 3.571A  pdb=" N   PHE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 395
      removed outlier: 3.671A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   THR A 388 " --> pdb=" O   MET A 384 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ILE A 389 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 426
      removed outlier: 3.815A  pdb=" N   ALA A 404 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   LEU A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ILE A 409 " --> pdb=" O   LEU A 405 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 415 " --> pdb=" O   THR A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 456
      removed outlier: 4.016A  pdb=" N   PHE A 439 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   LEU A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 441 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 7
      removed outlier: 3.605A  pdb=" N   VAL B   5 " --> pdb=" O   ALA B  23 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER B   7 " --> pdb=" O   SER B  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60
      removed outlier: 6.376A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   GLN B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   MET B  34 " --> pdb=" O   GLN B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 60
      removed outlier: 6.376A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   GLN B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   MET B  34 " --> pdb=" O   GLN B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 4.040A  pdb=" N   ARG B 104 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)

    250 hydrogen bonds defined for protein.
    729 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: 1.13

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 592
        1.27 -     1.41: 1172
        1.41 -     1.54: 2297
        1.54 -     1.68: 27
        1.68 -     1.81: 36
  Bond restraints: 4124
  Sorted by residual:
  bond pdb=" CAR 2TA A 601 "
       pdb=" CAS 2TA A 601 "
    ideal  model  delta    sigma   weight residual
    1.543  1.255  0.288 2.00e-02 2.50e+03 2.07e+02
  bond pdb=" CAO 2TA A 601 "
       pdb=" NAP 2TA A 601 "
    ideal  model  delta    sigma   weight residual
    1.444  1.194  0.250 2.00e-02 2.50e+03 1.56e+02
  bond pdb=" CAT 2TA A 601 "
       pdb=" NAP 2TA A 601 "
    ideal  model  delta    sigma   weight residual
    1.456  1.279  0.177 2.00e-02 2.50e+03 7.79e+01
  bond pdb=" C   ARG A 277 "
       pdb=" O   ARG A 277 "
    ideal  model  delta    sigma   weight residual
    1.237  1.136  0.100 1.16e-02 7.43e+03 7.48e+01
  bond pdb=" C2  2TA A 601 "
       pdb=" N1  2TA A 601 "
    ideal  model  delta    sigma   weight residual
    1.322  1.482 -0.160 2.00e-02 2.50e+03 6.39e+01
  ... (remaining 4119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 5578
        3.46 -     6.93: 43
        6.93 -    10.39: 2
       10.39 -    13.86: 1
       13.86 -    17.32: 2
  Bond angle restraints: 5626
  Sorted by residual:
  angle pdb=" N   VAL A  77 "
        pdb=" CA  VAL A  77 "
        pdb=" C   VAL A  77 "
      ideal   model   delta    sigma   weight residual
     110.05  101.20    8.85 1.09e+00 8.42e-01 6.59e+01
  angle pdb=" OBJ 2TA A 601 "
        pdb=" SBD 2TA A 601 "
        pdb=" OBK 2TA A 601 "
      ideal   model   delta    sigma   weight residual
     118.13  100.81   17.32 3.00e+00 1.11e-01 3.33e+01
  angle pdb=" CA  LEU A 190 "
        pdb=" C   LEU A 190 "
        pdb=" N   PRO A 191 "
      ideal   model   delta    sigma   weight residual
     118.23  123.02   -4.79 9.20e-01 1.18e+00 2.72e+01
  angle pdb=" C2  2TA A 601 "
        pdb=" NAF 2TA A 601 "
        pdb=" CAG 2TA A 601 "
      ideal   model   delta    sigma   weight residual
     131.32  116.30   15.02 3.00e+00 1.11e-01 2.51e+01
  angle pdb=" CA  VAL A  77 "
        pdb=" C   VAL A  77 "
        pdb=" O   VAL A  77 "
      ideal   model   delta    sigma   weight residual
     121.98  116.24    5.74 1.21e+00 6.83e-01 2.25e+01
  ... (remaining 5621 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.44: 2228
       29.44 -    58.89: 103
       58.89 -    88.33: 9
       88.33 -   117.77: 3
      117.77 -   147.22: 2
  Dihedral angle restraints: 2345
    sinusoidal: 873
      harmonic: 1472
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  155.56  -62.56     1      1.00e+01 1.00e-02 5.18e+01
  dihedral pdb=" CAG 2TA A 601 "
           pdb=" C2  2TA A 601 "
           pdb=" NAF 2TA A 601 "
           pdb=" N1  2TA A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.72 -147.94  147.22     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" CAI 2TA A 601 "
           pdb=" CAJ 2TA A 601 "
           pdb=" OAM 2TA A 601 "
           pdb=" CAN 2TA A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -1.36  129.06 -130.42     1      3.00e+01 1.11e-03 1.76e+01
  ... (remaining 2342 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 499
       0.048 -    0.096: 105
       0.096 -    0.144: 22
       0.144 -    0.192: 3
       0.192 -    0.240: 1
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  VAL A  77 "
            pdb=" N   VAL A  77 "
            pdb=" C   VAL A  77 "
            pdb=" CB  VAL A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  LEU A 190 "
            pdb=" N   LEU A 190 "
            pdb=" C   LEU A 190 "
            pdb=" CB  LEU A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" CA  LYS B  87 "
            pdb=" N   LYS B  87 "
            pdb=" C   LYS B  87 "
            pdb=" CB  LYS B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.39e-01
  ... (remaining 627 not shown)

  Planarity restraints: 683
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  80 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.41e+00
        pdb=" C   LYS A  80 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   LYS A  80 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PRO A  81 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 190 "    0.007 2.00e-02 2.50e+03   1.29e-02 1.66e+00
        pdb=" C   LEU A 190 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   LEU A 190 "    0.008 2.00e-02 2.50e+03
        pdb=" N   PRO A 191 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  13 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO B  14 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B  14 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  14 "    0.017 5.00e-02 4.00e+02
  ... (remaining 680 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1339
        2.83 -     3.35: 3715
        3.35 -     3.87: 6532
        3.87 -     4.38: 8047
        4.38 -     4.90: 13737
  Nonbonded interactions: 33370
  Sorted by model distance:
  nonbonded pdb=" O   SER A  89 "
            pdb=" OG1 THR A  93 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" N   VAL A  77 "
            pdb=" O   VAL A  77 "
     model   vdw
     2.422 2.496
  nonbonded pdb=" N   ASN A 340 "
            pdb=" OD1 ASN A 340 "
     model   vdw
     2.428 3.120
  nonbonded pdb=" O   ASP B  73 "
            pdb=" OD1 ASP B  73 "
     model   vdw
     2.432 3.040
  nonbonded pdb=" NAP 2TA A 601 "
            pdb=" OAM 2TA A 601 "
     model   vdw
     2.452 2.496
  ... (remaining 33365 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.460
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.060
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
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      :  0.012   0.288   4125  Z= 0.633
  Angle     :  0.836  17.323   5628  Z= 0.478
  Chirality :  0.043   0.240    630
  Planarity :  0.004   0.030    683
  Dihedral  : 17.300 147.216   1406
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 19.48 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.36), residues: 496
  helix: -1.25 (0.29), residues: 275
  sheet: -1.31 (0.86), residues: 43
  loop : -0.91 (0.46), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 110 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.007   0.001   PHE A 439 
 TYR   0.013   0.001   TYR A 336 
 ARG   0.003   0.001   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25401 (  239)
  hydrogen bonds       : angle       8.95753 (  729)
  SS BOND              : bond        0.00698 (    1)
  SS BOND              : angle       1.15500 (    2)
  covalent geometry    : bond        0.01236 ( 4124)
  covalent geometry    : angle       0.83570 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.1972
  time to fit residues: 14.6191
Evaluate side-chains
  58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 12 optimal weight:    0.3980
   chunk 25 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.153799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.137177 restraints weight = 4911.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.48
r_work: 0.3327 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4125  Z= 0.182
  Angle     :  0.615   6.583   5628  Z= 0.319
  Chirality :  0.043   0.146    630
  Planarity :  0.005   0.038    683
  Dihedral  : 11.603 153.736    571
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 17.10 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.37), residues: 496
  helix:  0.39 (0.30), residues: 293
  sheet: -0.78 (0.83), residues: 45
  loop : -0.99 (0.45), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.013   0.002   PHE A 292 
 TYR   0.009   0.001   TYR A 336 
 ARG   0.007   0.001   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05256 (  239)
  hydrogen bonds       : angle       4.53702 (  729)
  SS BOND              : bond        0.00960 (    1)
  SS BOND              : angle       1.61279 (    2)
  covalent geometry    : bond        0.00425 ( 4124)
  covalent geometry    : angle       0.61471 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.453 
Fit side-chains
REVERT: B   52 SER cc_start: 0.8402 (m) cc_final: 0.8132 (t)
REVERT: A  385 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8567 (tt)
  outliers start: 19
  outliers final: 10
  residues processed: 69
  average time/residue: 0.1233
  time to fit residues: 11.5647
Evaluate side-chains
  69 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  452 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.149190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.132831 restraints weight = 4917.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.45
r_work: 0.3279 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.074   4125  Z= 0.274
  Angle     :  0.682   6.550   5628  Z= 0.353
  Chirality :  0.046   0.165    630
  Planarity :  0.005   0.047    683
  Dihedral  : 12.132 152.283    568
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 16.39 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.38), residues: 496
  helix:  0.69 (0.31), residues: 291
  sheet: -0.77 (0.77), residues: 51
  loop : -1.18 (0.46), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  94 
 HIS   0.005   0.002   HIS A 200 
 PHE   0.013   0.002   PHE A 439 
 TYR   0.014   0.002   TYR A 336 
 ARG   0.006   0.001   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05853 (  239)
  hydrogen bonds       : angle       4.54091 (  729)
  SS BOND              : bond        0.01340 (    1)
  SS BOND              : angle       2.24252 (    2)
  covalent geometry    : bond        0.00667 ( 4124)
  covalent geometry    : angle       0.68050 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.430 
Fit side-chains
REVERT: B   52 SER cc_start: 0.8491 (m) cc_final: 0.8269 (t)
REVERT: B   86 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6684 (mp)
REVERT: A  194 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7109 (mptt)
REVERT: A  385 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8652 (tt)
  outliers start: 28
  outliers final: 22
  residues processed: 75
  average time/residue: 0.1258
  time to fit residues: 12.5781
Evaluate side-chains
  80 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 55
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  452 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 47 optimal weight:    0.3980
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.2980
   chunk 48 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.152445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.136094 restraints weight = 4931.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.47
r_work: 0.3349 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4125  Z= 0.161
  Angle     :  0.560   6.157   5628  Z= 0.292
  Chirality :  0.041   0.152    630
  Planarity :  0.005   0.049    683
  Dihedral  : 11.586 150.829    568
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 18.29 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.38), residues: 496
  helix:  1.10 (0.32), residues: 293
  sheet: -0.40 (0.79), residues: 45
  loop : -1.10 (0.46), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.011   0.001   PHE A 439 
 TYR   0.010   0.001   TYR A 336 
 ARG   0.001   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04651 (  239)
  hydrogen bonds       : angle       4.15239 (  729)
  SS BOND              : bond        0.00817 (    1)
  SS BOND              : angle       1.64972 (    2)
  covalent geometry    : bond        0.00376 ( 4124)
  covalent geometry    : angle       0.55961 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.421 
Fit side-chains
REVERT: B   52 SER cc_start: 0.8406 (m) cc_final: 0.8140 (t)
REVERT: A  194 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6948 (mptt)
REVERT: A  385 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8581 (tt)
  outliers start: 24
  outliers final: 17
  residues processed: 72
  average time/residue: 0.1233
  time to fit residues: 11.7607
Evaluate side-chains
  75 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.150652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.134323 restraints weight = 5052.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.47
r_work: 0.3312 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   4125  Z= 0.199
  Angle     :  0.593   6.002   5628  Z= 0.308
  Chirality :  0.043   0.158    630
  Planarity :  0.005   0.050    683
  Dihedral  : 11.625 150.936    568
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  7.60 %
    Allowed  : 16.86 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.38), residues: 496
  helix:  1.12 (0.31), residues: 293
  sheet: -0.27 (0.76), residues: 50
  loop : -1.21 (0.45), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.015   0.002   PHE A 439 
 TYR   0.010   0.001   TYR B 112 
 ARG   0.002   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04922 (  239)
  hydrogen bonds       : angle       4.20641 (  729)
  SS BOND              : bond        0.01086 (    1)
  SS BOND              : angle       2.08473 (    2)
  covalent geometry    : bond        0.00479 ( 4124)
  covalent geometry    : angle       0.59183 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 57
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6797 (mptt)
REVERT: A  385 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8668 (tt)
  outliers start: 32
  outliers final: 23
  residues processed: 78
  average time/residue: 0.1201
  time to fit residues: 12.5003
Evaluate side-chains
  78 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 53
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  452 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0980
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 118 GLN
A 200 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.151601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.135302 restraints weight = 4977.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.45
r_work: 0.3337 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4125  Z= 0.175
  Angle     :  0.565   6.221   5628  Z= 0.293
  Chirality :  0.042   0.154    630
  Planarity :  0.005   0.050    683
  Dihedral  : 11.512 150.151    568
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 17.58 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.38), residues: 496
  helix:  1.24 (0.31), residues: 293
  sheet: -0.06 (0.76), residues: 45
  loop : -1.26 (0.44), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  94 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.020   0.002   PHE A 439 
 TYR   0.009   0.001   TYR B 112 
 ARG   0.001   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04640 (  239)
  hydrogen bonds       : angle       4.08860 (  729)
  SS BOND              : bond        0.00948 (    1)
  SS BOND              : angle       1.89216 (    2)
  covalent geometry    : bond        0.00415 ( 4124)
  covalent geometry    : angle       0.56382 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 54
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6794 (mptt)
  outliers start: 29
  outliers final: 25
  residues processed: 75
  average time/residue: 0.1245
  time to fit residues: 12.5319
Evaluate side-chains
  80 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 54
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.149572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.133199 restraints weight = 5004.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.45
r_work: 0.3310 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   4125  Z= 0.206
  Angle     :  0.593   6.174   5628  Z= 0.309
  Chirality :  0.044   0.159    630
  Planarity :  0.005   0.050    683
  Dihedral  : 11.663 150.492    568
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 19.00 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.38), residues: 496
  helix:  1.20 (0.31), residues: 293
  sheet: -0.24 (0.74), residues: 49
  loop : -1.32 (0.44), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.018   0.002   PHE A 439 
 TYR   0.012   0.001   TYR B 112 
 ARG   0.002   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04939 (  239)
  hydrogen bonds       : angle       4.17397 (  729)
  SS BOND              : bond        0.01174 (    1)
  SS BOND              : angle       2.19968 (    2)
  covalent geometry    : bond        0.00499 ( 4124)
  covalent geometry    : angle       0.59165 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 53
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A   27 MET cc_start: 0.9134 (mmm) cc_final: 0.8893 (mmm)
REVERT: A  194 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6824 (mptt)
  outliers start: 27
  outliers final: 25
  residues processed: 71
  average time/residue: 0.1238
  time to fit residues: 11.7052
Evaluate side-chains
  78 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 52
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  452 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.150764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.134602 restraints weight = 4990.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.43
r_work: 0.3311 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   4125  Z= 0.188
  Angle     :  0.570   6.335   5628  Z= 0.297
  Chirality :  0.043   0.157    630
  Planarity :  0.005   0.050    683
  Dihedral  : 11.545 149.876    568
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 18.53 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.38), residues: 496
  helix:  1.25 (0.31), residues: 293
  sheet: -0.16 (0.73), residues: 49
  loop : -1.29 (0.45), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  94 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.017   0.002   PHE A 439 
 TYR   0.010   0.001   TYR B 112 
 ARG   0.001   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04718 (  239)
  hydrogen bonds       : angle       4.09966 (  729)
  SS BOND              : bond        0.01051 (    1)
  SS BOND              : angle       2.08099 (    2)
  covalent geometry    : bond        0.00451 ( 4124)
  covalent geometry    : angle       0.56859 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 53
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6747 (mptt)
  outliers start: 29
  outliers final: 26
  residues processed: 72
  average time/residue: 0.1309
  time to fit residues: 12.7251
Evaluate side-chains
  79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 52
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.150489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.133826 restraints weight = 4998.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.49
r_work: 0.3298 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   4125  Z= 0.202
  Angle     :  0.587   6.395   5628  Z= 0.306
  Chirality :  0.043   0.159    630
  Planarity :  0.005   0.050    683
  Dihedral  : 11.633 150.113    568
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 18.76 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.38), residues: 496
  helix:  1.23 (0.31), residues: 293
  sheet: -0.36 (0.71), residues: 56
  loop : -1.26 (0.46), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.017   0.002   PHE A 439 
 TYR   0.012   0.001   TYR B 112 
 ARG   0.002   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04891 (  239)
  hydrogen bonds       : angle       4.13750 (  729)
  SS BOND              : bond        0.01117 (    1)
  SS BOND              : angle       2.21741 (    2)
  covalent geometry    : bond        0.00487 ( 4124)
  covalent geometry    : angle       0.58608 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 53
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6819 (mptt)
  outliers start: 27
  outliers final: 26
  residues processed: 71
  average time/residue: 0.1269
  time to fit residues: 12.0085
Evaluate side-chains
  80 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 53
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain A residue   45 GLN
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 48 optimal weight:    0.2980
   chunk 19 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 8 optimal weight:    0.3980
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   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 = 0.3621 r_free = 0.3621 target = 0.152433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.136416 restraints weight = 4962.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.43
r_work: 0.3365 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4125  Z= 0.156
  Angle     :  0.542   6.227   5628  Z= 0.282
  Chirality :  0.042   0.152    630
  Planarity :  0.005   0.050    683
  Dihedral  : 11.418 149.384    568
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 19.24 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.38), residues: 496
  helix:  1.40 (0.31), residues: 293
  sheet: -0.23 (0.72), residues: 51
  loop : -1.19 (0.46), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  94 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.015   0.001   PHE A 439 
 TYR   0.010   0.001   TYR B 112 
 ARG   0.001   0.000   ARG A 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04401 (  239)
  hydrogen bonds       : angle       3.99190 (  729)
  SS BOND              : bond        0.00882 (    1)
  SS BOND              : angle       1.80575 (    2)
  covalent geometry    : bond        0.00366 ( 4124)
  covalent geometry    : angle       0.54116 ( 5626)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 56
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6705 (mptt)
  outliers start: 25
  outliers final: 22
  residues processed: 71
  average time/residue: 0.1206
  time to fit residues: 11.4178
Evaluate side-chains
  79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 33 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0980
   chunk 40 optimal weight:    0.0980
   chunk 2 optimal weight:    0.0770
   overall best weight:    0.3338

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

Flipped N/Q/H residues before XYZ refinement:
B 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.154553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.138501 restraints weight = 4985.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.43
r_work: 0.3395 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4125  Z= 0.124
  Angle     :  0.508   6.086   5628  Z= 0.264
  Chirality :  0.040   0.142    630
  Planarity :  0.004   0.049    683
  Dihedral  : 11.239 148.658    568
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 19.71 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.38), residues: 496
  helix:  1.67 (0.31), residues: 293
  sheet: -0.15 (0.73), residues: 51
  loop : -1.12 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.018   0.001   PHE A 439 
 TYR   0.008   0.001   TYR B 112 
 ARG   0.002   0.000   ARG A 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  239)
  hydrogen bonds       : angle       3.84290 (  729)
  SS BOND              : bond        0.00672 (    1)
  SS BOND              : angle       1.37714 (    2)
  covalent geometry    : bond        0.00279 ( 4124)
  covalent geometry    : angle       0.50699 ( 5626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2588.60 seconds
wall clock time: 44 minutes 56.22 seconds (2696.22 seconds total)