Starting phenix.real_space_refine
on Fri May  9 21:28:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zan_39881/05_2025/8zan_39881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zan_39881/05_2025/8zan_39881.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zan_39881/05_2025/8zan_39881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zan_39881/05_2025/8zan_39881.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zan_39881/05_2025/8zan_39881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zan_39881/05_2025/8zan_39881.cif"
  }
  resolution = 2.4
  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=   0.007
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      34      5.16       5
     C    2618      2.51       5
     N     632      2.21       5
     O     654      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3938
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1949
          Classifications: {'peptide': 246}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 1949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1949
          Classifications: {'peptide': 246}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 6.85, per 1000 atoms: 1.74
  Number of scatterers: 3938
  At special positions: 0
  Unit cell: (60.55, 72.45, 80.15, 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      34     16.00
     O     654      8.00
     N     632      7.00
     C    2618      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  34 " - pdb=" SG  CYS B  36 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS B  34 " 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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 454.8 milliseconds
  

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  884

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      82.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 40
    Processing helix  chain 'A' and resid 47 through 77
    Processing helix  chain 'A' and resid 80 through 101
      removed outlier: 3.900A  pdb=" N   ILE A  84 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU A 101 " --> pdb=" O   GLU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 136
      removed outlier: 3.575A  pdb=" N   TYR A 121 " --> pdb=" O   GLN A 117 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
    Processing helix  chain 'A' and resid 146 through 168
    Processing helix  chain 'A' and resid 171 through 203
    Processing helix  chain 'A' and resid 206 through 233
      Proline residue:  A 227  - end of helix
    Processing helix  chain 'A' and resid 240 through 257
    Processing helix  chain 'A' and resid 257 through 278
    Processing helix  chain 'B' and resid 36 through 40
    Processing helix  chain 'B' and resid 47 through 77
    Processing helix  chain 'B' and resid 80 through 101
      removed outlier: 3.900A  pdb=" N   ILE B  84 " --> pdb=" O   GLY B  80 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU B 101 " --> pdb=" O   GLU B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 136
      removed outlier: 3.575A  pdb=" N   TYR B 121 " --> pdb=" O   GLN B 117 " (cutoff:3.500A)
      Proline residue:  B 129  - end of helix
    Processing helix  chain 'B' and resid 146 through 168
    Processing helix  chain 'B' and resid 171 through 203
    Processing helix  chain 'B' and resid 206 through 233
      Proline residue:  B 227  - end of helix
    Processing helix  chain 'B' and resid 240 through 257
    Processing helix  chain 'B' and resid 257 through 278

    316 hydrogen bonds defined for protein.
    936 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: 1.03

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1164
        1.34 -     1.46: 1178
        1.46 -     1.58: 1668
        1.58 -     1.70: 0
        1.70 -     1.82: 50
  Bond restraints: 4060
  Sorted by residual:
  bond pdb=" C   TYR B  35 "
       pdb=" O   TYR B  35 "
    ideal  model  delta    sigma   weight residual
    1.234  1.247 -0.013 8.30e-03 1.45e+04 2.40e+00
  bond pdb=" C   TYR A  35 "
       pdb=" O   TYR A  35 "
    ideal  model  delta    sigma   weight residual
    1.234  1.247 -0.012 8.30e-03 1.45e+04 2.22e+00
  bond pdb=" N   TYR A  35 "
       pdb=" CA  TYR A  35 "
    ideal  model  delta    sigma   weight residual
    1.468  1.454  0.014 1.24e-02 6.50e+03 1.30e+00
  bond pdb=" N   TYR B  35 "
       pdb=" CA  TYR B  35 "
    ideal  model  delta    sigma   weight residual
    1.468  1.454  0.014 1.24e-02 6.50e+03 1.29e+00
  bond pdb=" C   ASN B 104 "
       pdb=" N   PRO B 105 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.28e+00
  ... (remaining 4055 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 5348
        1.59 -     3.19: 148
        3.19 -     4.78: 20
        4.78 -     6.38: 4
        6.38 -     7.97: 6
  Bond angle restraints: 5526
  Sorted by residual:
  angle pdb=" N   SER B 106 "
        pdb=" CA  SER B 106 "
        pdb=" C   SER B 106 "
      ideal   model   delta    sigma   weight residual
     114.62  108.55    6.07 1.14e+00 7.69e-01 2.83e+01
  angle pdb=" N   SER A 106 "
        pdb=" CA  SER A 106 "
        pdb=" C   SER A 106 "
      ideal   model   delta    sigma   weight residual
     114.62  108.55    6.07 1.14e+00 7.69e-01 2.83e+01
  angle pdb=" CA  PRO A 105 "
        pdb=" N   PRO A 105 "
        pdb=" CD  PRO A 105 "
      ideal   model   delta    sigma   weight residual
     112.00  106.01    5.99 1.40e+00 5.10e-01 1.83e+01
  angle pdb=" CA  PRO B 105 "
        pdb=" N   PRO B 105 "
        pdb=" CD  PRO B 105 "
      ideal   model   delta    sigma   weight residual
     112.00  106.01    5.99 1.40e+00 5.10e-01 1.83e+01
  angle pdb=" C   ALA B 169 "
        pdb=" N   THR B 170 "
        pdb=" CA  THR B 170 "
      ideal   model   delta    sigma   weight residual
     121.54  128.12   -6.58 1.91e+00 2.74e-01 1.19e+01
  ... (remaining 5521 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.46: 1847
       15.46 -    30.92: 286
       30.92 -    46.38: 89
       46.38 -    61.84: 24
       61.84 -    77.30: 6
  Dihedral angle restraints: 2252
    sinusoidal: 852
      harmonic: 1400
  Sorted by residual:
  dihedral pdb=" CA  ASN B 104 "
           pdb=" C   ASN B 104 "
           pdb=" N   PRO B 105 "
           pdb=" CA  PRO B 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.91  -28.09     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  ASN A 104 "
           pdb=" C   ASN A 104 "
           pdb=" N   PRO A 105 "
           pdb=" CA  PRO A 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.94  -28.06     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CB  CYS A  36 "
           pdb=" SG  CYS A  36 "
           pdb=" SG  CYS B  34 "
           pdb=" CB  CYS B  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.82   33.18     1      1.00e+01 1.00e-02 1.57e+01
  ... (remaining 2249 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 487
       0.049 -    0.097: 103
       0.097 -    0.145: 10
       0.145 -    0.194: 2
       0.194 -    0.242: 2
  Chirality restraints: 604
  Sorted by residual:
  chirality pdb=" CA  PRO A 105 "
            pdb=" N   PRO A 105 "
            pdb=" C   PRO A 105 "
            pdb=" CB  PRO A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  PRO B 105 "
            pdb=" N   PRO B 105 "
            pdb=" C   PRO B 105 "
            pdb=" CB  PRO B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CA  THR A 170 "
            pdb=" N   THR A 170 "
            pdb=" C   THR A 170 "
            pdb=" CB  THR A 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.58e-01
  ... (remaining 601 not shown)

  Planarity restraints: 668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 104 "    0.094 5.00e-02 4.00e+02   1.42e-01 3.23e+01
        pdb=" N   PRO B 105 "   -0.246 5.00e-02 4.00e+02
        pdb=" CA  PRO B 105 "    0.078 5.00e-02 4.00e+02
        pdb=" CD  PRO B 105 "    0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 104 "   -0.094 5.00e-02 4.00e+02   1.42e-01 3.22e+01
        pdb=" N   PRO A 105 "    0.245 5.00e-02 4.00e+02
        pdb=" CA  PRO A 105 "   -0.078 5.00e-02 4.00e+02
        pdb=" CD  PRO A 105 "   -0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 203 "   -0.020 5.00e-02 4.00e+02   2.99e-02 1.43e+00
        pdb=" N   PRO A 204 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 204 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 204 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 665 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1281
        2.83 -     3.35: 3947
        3.35 -     3.86: 7622
        3.86 -     4.38: 8473
        4.38 -     4.90: 13995
  Nonbonded interactions: 35318
  Sorted by model distance:
  nonbonded pdb=" O   THR A 246 "
            pdb=" OG1 THR A 250 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   THR B 246 "
            pdb=" OG1 THR B 250 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   MET A 168 "
            pdb=" ND2 ASN B 104 "
     model   vdw
     2.345 3.120
  nonbonded pdb=" ND2 ASN A 104 "
            pdb=" O   MET B 168 "
     model   vdw
     2.345 3.120
  nonbonded pdb=" O   ASN B  46 "
            pdb=" ND2 ASN B  46 "
     model   vdw
     2.363 3.120
  ... (remaining 35313 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             12.840
  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:          0.360
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     17.590
  Find NCS groups from input model:        0.070
  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:11.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
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      :  0.003   0.027   4066  Z= 0.171
  Angle     :  0.651   7.970   5530  Z= 0.387
  Chirality :  0.042   0.242    604
  Planarity :  0.008   0.142    668
  Dihedral  : 17.049  77.298   1362
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  1.23 %
    Allowed  :  5.33 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 19.70 %
    Favored  : 77.34 %
  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:  1.81 (0.39), residues: 488
  helix:  2.21 (0.26), residues: 372
  sheet:  None (None), residues: 0
  loop : -2.36 (0.56), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  75 
 HIS   0.002   0.001   HIS B 114 
 PHE   0.010   0.002   PHE B 178 
 TYR   0.011   0.001   TYR A 109 
 ARG   0.002   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11505 (  316)
  hydrogen bonds       : angle       5.26418 (  936)
  SS BOND              : bond        0.00297 (    2)
  SS BOND              : angle       1.04719 (    4)
  covalent geometry    : bond        0.00346 ( 4060)
  covalent geometry    : angle       0.65013 ( 5526)
  Misc. bond           : bond        0.00192 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8245 (mt0)
REVERT: A   93 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8075 (tmmm)
REVERT: A  194 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7770 (mmtt)
REVERT: B   56 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8248 (mt0)
REVERT: B   93 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8070 (tmmm)
REVERT: B  194 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7660 (mtpm)
  outliers start: 12
  outliers final: 6
  residues processed: 56
  average time/residue: 1.2494
  time to fit residues: 72.3325
Evaluate side-chains
  56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue   56 GLN
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  155 SER
Chi-restraints excluded: chain B residue  276 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
B  46 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.124040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.108687 restraints weight = 4140.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.55
r_work: 0.3186 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.0711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4066  Z= 0.178
  Angle     :  0.616   8.367   5530  Z= 0.333
  Chirality :  0.043   0.249    604
  Planarity :  0.009   0.143    668
  Dihedral  :  7.293  52.435    574
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  5.33 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.70 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    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:  1.79 (0.39), residues: 488
  helix:  2.10 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.33 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  75 
 HIS   0.002   0.001   HIS A 201 
 PHE   0.011   0.002   PHE B 178 
 TYR   0.015   0.001   TYR A 109 
 ARG   0.001   0.000   ARG B 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04669 (  316)
  hydrogen bonds       : angle       4.78724 (  936)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       0.52039 (    4)
  covalent geometry    : bond        0.00386 ( 4060)
  covalent geometry    : angle       0.61598 ( 5526)
  Misc. bond           : bond        0.00185 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  103 LYS cc_start: 0.7533 (mmtm) cc_final: 0.6856 (mtpt)
REVERT: A  194 LYS cc_start: 0.7741 (mtpt) cc_final: 0.6947 (mmtt)
REVERT: A  273 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6352 (tp30)
REVERT: B  103 LYS cc_start: 0.7523 (mmtm) cc_final: 0.6839 (mtpt)
REVERT: B  194 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6781 (mtpm)
REVERT: B  273 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6330 (tp30)
  outliers start: 6
  outliers final: 4
  residues processed: 57
  average time/residue: 1.3805
  time to fit residues: 81.1651
Evaluate side-chains
  57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 ARG
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  147 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
B  46 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.124556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.109508 restraints weight = 4153.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.47
r_work: 0.3165 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.0816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4066  Z= 0.162
  Angle     :  0.592   8.415   5530  Z= 0.317
  Chirality :  0.042   0.246    604
  Planarity :  0.008   0.143    668
  Dihedral  :  6.402  53.963    554
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  6.56 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.23 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    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:  1.86 (0.39), residues: 488
  helix:  2.16 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.34 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 118 
 HIS   0.002   0.001   HIS A 201 
 PHE   0.010   0.002   PHE A 178 
 TYR   0.014   0.001   TYR A 109 
 ARG   0.001   0.000   ARG B 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04520 (  316)
  hydrogen bonds       : angle       4.75975 (  936)
  SS BOND              : bond        0.00108 (    2)
  SS BOND              : angle       0.64222 (    4)
  covalent geometry    : bond        0.00348 ( 4060)
  covalent geometry    : angle       0.59149 ( 5526)
  Misc. bond           : bond        0.00164 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A  103 LYS cc_start: 0.7171 (mmtm) cc_final: 0.6490 (mtpt)
REVERT: A  194 LYS cc_start: 0.7421 (mtpt) cc_final: 0.6568 (mmtt)
REVERT: A  273 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6129 (tp30)
REVERT: B  103 LYS cc_start: 0.7172 (mmtm) cc_final: 0.6488 (mtpt)
REVERT: B  194 LYS cc_start: 0.7092 (mmmt) cc_final: 0.6402 (mtpm)
REVERT: B  273 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6093 (tp30)
  outliers start: 10
  outliers final: 2
  residues processed: 58
  average time/residue: 1.3391
  time to fit residues: 80.2287
Evaluate side-chains
  56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain B residue  139 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 47 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:
A  46 ASN
A 143 ASN
B  46 ASN
B 143 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.124190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.109165 restraints weight = 4128.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.47
r_work: 0.3162 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4066  Z= 0.164
  Angle     :  0.596   8.511   5530  Z= 0.318
  Chirality :  0.042   0.247    604
  Planarity :  0.008   0.143    668
  Dihedral  :  6.316  52.659    554
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  6.56 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.21 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    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:  1.88 (0.39), residues: 488
  helix:  2.19 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.39 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 118 
 HIS   0.002   0.001   HIS A 201 
 PHE   0.010   0.002   PHE A 178 
 TYR   0.014   0.001   TYR A 109 
 ARG   0.001   0.000   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04485 (  316)
  hydrogen bonds       : angle       4.72301 (  936)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       0.61300 (    4)
  covalent geometry    : bond        0.00350 ( 4060)
  covalent geometry    : angle       0.59586 ( 5526)
  Misc. bond           : bond        0.00165 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A  103 LYS cc_start: 0.7165 (mmtm) cc_final: 0.6500 (mtpt)
REVERT: A  194 LYS cc_start: 0.7413 (mtpt) cc_final: 0.6554 (mmtt)
REVERT: A  273 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6134 (tp30)
REVERT: B  103 LYS cc_start: 0.7172 (mmtm) cc_final: 0.6503 (mtpt)
REVERT: B  194 LYS cc_start: 0.7069 (mmmt) cc_final: 0.6371 (mtpm)
REVERT: B  273 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6106 (tp30)
  outliers start: 8
  outliers final: 0
  residues processed: 62
  average time/residue: 1.3053
  time to fit residues: 83.5458
Evaluate side-chains
  55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0000
   chunk 24 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
A 104 ASN
B  46 ASN
B 104 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.126383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.111397 restraints weight = 4301.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.51
r_work: 0.3184 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.0974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4066  Z= 0.148
  Angle     :  0.575   8.013   5530  Z= 0.307
  Chirality :  0.042   0.248    604
  Planarity :  0.008   0.141    668
  Dihedral  :  6.123  54.653    552
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.97 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 18.97 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    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:  1.93 (0.39), residues: 488
  helix:  2.26 (0.26), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.43 (0.57), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 118 
 HIS   0.002   0.001   HIS A 201 
 PHE   0.010   0.001   PHE A 219 
 TYR   0.012   0.001   TYR A 109 
 ARG   0.000   0.000   ARG A 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04265 (  316)
  hydrogen bonds       : angle       4.70851 (  936)
  SS BOND              : bond        0.00311 (    2)
  SS BOND              : angle       2.29111 (    4)
  covalent geometry    : bond        0.00314 ( 4060)
  covalent geometry    : angle       0.57183 ( 5526)
  Misc. bond           : bond        0.00127 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7596 (mt0)
REVERT: A  103 LYS cc_start: 0.7184 (mmtm) cc_final: 0.6511 (mtpt)
REVERT: A  194 LYS cc_start: 0.7406 (mtpt) cc_final: 0.6548 (mmtt)
REVERT: A  273 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6127 (tp30)
REVERT: B   56 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7589 (mt0)
REVERT: B  103 LYS cc_start: 0.7195 (mmtm) cc_final: 0.6518 (mtpt)
REVERT: B  194 LYS cc_start: 0.7074 (mmmt) cc_final: 0.6379 (mtpm)
REVERT: B  273 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6103 (tp30)
  outliers start: 9
  outliers final: 3
  residues processed: 59
  average time/residue: 1.3206
  time to fit residues: 80.3814
Evaluate side-chains
  59 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   56 GLN
Chi-restraints excluded: chain B residue  276 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 30 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
A 104 ASN
A 137 ASN
B  46 ASN
B 104 ASN
B 137 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.122863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.107790 restraints weight = 4193.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 1.48
r_work: 0.3144 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.0994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4066  Z= 0.185
  Angle     :  0.624   9.687   5530  Z= 0.329
  Chirality :  0.043   0.236    604
  Planarity :  0.009   0.146    668
  Dihedral  :  6.134  49.480    552
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  7.38 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 17.73 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    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:  1.85 (0.38), residues: 488
  helix:  2.19 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.48 (0.56), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 118 
 HIS   0.003   0.001   HIS A 201 
 PHE   0.012   0.002   PHE B 178 
 TYR   0.014   0.001   TYR A 109 
 ARG   0.001   0.000   ARG A 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04592 (  316)
  hydrogen bonds       : angle       4.77478 (  936)
  SS BOND              : bond        0.00493 (    2)
  SS BOND              : angle       1.67416 (    4)
  covalent geometry    : bond        0.00403 ( 4060)
  covalent geometry    : angle       0.62210 ( 5526)
  Misc. bond           : bond        0.00191 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7595 (mt0)
REVERT: A  103 LYS cc_start: 0.7250 (mmtm) cc_final: 0.6600 (mtpt)
REVERT: A  194 LYS cc_start: 0.7430 (mtpt) cc_final: 0.6570 (mmtt)
REVERT: A  273 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6164 (tp30)
REVERT: B   56 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7594 (mt0)
REVERT: B  103 LYS cc_start: 0.7263 (mmtm) cc_final: 0.6608 (mtpt)
REVERT: B  194 LYS cc_start: 0.7081 (mmmt) cc_final: 0.6366 (mtpm)
REVERT: B  273 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6144 (tp30)
  outliers start: 14
  outliers final: 6
  residues processed: 60
  average time/residue: 1.2963
  time to fit residues: 80.2751
Evaluate side-chains
  60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 CYS
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   56 GLN
Chi-restraints excluded: chain B residue  100 PHE
Chi-restraints excluded: chain B residue  139 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0070
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.6800

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
A 104 ASN
B  46 ASN
B 104 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.124450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.109455 restraints weight = 4200.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.49
r_work: 0.3163 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4066  Z= 0.158
  Angle     :  0.615  10.833   5530  Z= 0.321
  Chirality :  0.042   0.230    604
  Planarity :  0.009   0.150    668
  Dihedral  :  6.199  53.090    552
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.97 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.73 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.38), residues: 488
  helix:  2.25 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.34 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 118 
 HIS   0.002   0.001   HIS B 201 
 PHE   0.010   0.002   PHE A 178 
 TYR   0.013   0.001   TYR A 109 
 ARG   0.001   0.000   ARG B 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  316)
  hydrogen bonds       : angle       4.72226 (  936)
  SS BOND              : bond        0.00256 (    2)
  SS BOND              : angle       1.17684 (    4)
  covalent geometry    : bond        0.00329 ( 4060)
  covalent geometry    : angle       0.61418 ( 5526)
  Misc. bond           : bond        0.00153 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7554 (mt0)
REVERT: A  103 LYS cc_start: 0.7220 (mmtm) cc_final: 0.6587 (mtpt)
REVERT: A  194 LYS cc_start: 0.7400 (mtpt) cc_final: 0.6539 (mmtt)
REVERT: A  273 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6125 (tp30)
REVERT: B   56 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7562 (mt0)
REVERT: B  103 LYS cc_start: 0.7221 (mmtm) cc_final: 0.6587 (mtpt)
REVERT: B  194 LYS cc_start: 0.7069 (mmmt) cc_final: 0.6356 (mtpm)
REVERT: B  273 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6108 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 62
  average time/residue: 1.3055
  time to fit residues: 83.5589
Evaluate side-chains
  64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 CYS
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   56 GLN
Chi-restraints excluded: chain B residue  100 PHE
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  276 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0670
   chunk 23 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
B  46 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.125894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.110946 restraints weight = 4186.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.50
r_work: 0.3182 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4066  Z= 0.144
  Angle     :  0.599  11.147   5530  Z= 0.310
  Chirality :  0.041   0.233    604
  Planarity :  0.009   0.150    668
  Dihedral  :  6.133  53.812    552
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.97 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.72 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    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 (0.39), residues: 488
  helix:  2.32 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.34 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 118 
 HIS   0.002   0.001   HIS B 201 
 PHE   0.010   0.002   PHE A 219 
 TYR   0.013   0.001   TYR A 109 
 ARG   0.001   0.000   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04255 (  316)
  hydrogen bonds       : angle       4.66000 (  936)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       1.00968 (    4)
  covalent geometry    : bond        0.00294 ( 4060)
  covalent geometry    : angle       0.59888 ( 5526)
  Misc. bond           : bond        0.00133 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7539 (mt0)
REVERT: A  103 LYS cc_start: 0.7274 (mmtm) cc_final: 0.6646 (mtpt)
REVERT: A  194 LYS cc_start: 0.7397 (mtpt) cc_final: 0.6534 (mmtt)
REVERT: A  273 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6124 (tp30)
REVERT: B   56 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7543 (mt0)
REVERT: B  103 LYS cc_start: 0.7271 (mmtm) cc_final: 0.6641 (mtpt)
REVERT: B  194 LYS cc_start: 0.7062 (mmmt) cc_final: 0.6465 (mmtt)
REVERT: B  273 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6110 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 60
  average time/residue: 1.1731
  time to fit residues: 72.8735
Evaluate side-chains
  63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 CYS
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   56 GLN
Chi-restraints excluded: chain B residue  100 PHE
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  276 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
B  46 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.122868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.108322 restraints weight = 4232.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.43
r_work: 0.3146 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4066  Z= 0.178
  Angle     :  0.642  11.733   5530  Z= 0.332
  Chirality :  0.043   0.233    604
  Planarity :  0.009   0.152    668
  Dihedral  :  6.164  50.626    552
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.97 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.72 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    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 (0.38), residues: 488
  helix:  2.25 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.32 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 118 
 HIS   0.003   0.001   HIS B 201 
 PHE   0.012   0.002   PHE A 178 
 TYR   0.014   0.001   TYR A 109 
 ARG   0.001   0.000   ARG B 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04540 (  316)
  hydrogen bonds       : angle       4.74751 (  936)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       1.16981 (    4)
  covalent geometry    : bond        0.00384 ( 4060)
  covalent geometry    : angle       0.64191 ( 5526)
  Misc. bond           : bond        0.00181 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7515 (mt0)
REVERT: A  103 LYS cc_start: 0.7238 (mmtm) cc_final: 0.6579 (mtpt)
REVERT: A  194 LYS cc_start: 0.7336 (mtpt) cc_final: 0.6478 (mmtt)
REVERT: A  273 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6139 (tp30)
REVERT: B   56 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7528 (mt0)
REVERT: B  103 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6591 (mtpt)
REVERT: B  194 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6304 (mtpm)
REVERT: B  273 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6122 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 57
  average time/residue: 1.1985
  time to fit residues: 70.6765
Evaluate side-chains
  61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 CYS
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   56 GLN
Chi-restraints excluded: chain B residue  100 PHE
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  276 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
B  46 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.124221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.109522 restraints weight = 4200.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.46
r_work: 0.3163 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4066  Z= 0.155
  Angle     :  0.623  11.726   5530  Z= 0.321
  Chirality :  0.042   0.236    604
  Planarity :  0.009   0.152    668
  Dihedral  :  6.185  53.528    552
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.56 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.72 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    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 (0.38), residues: 488
  helix:  2.29 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.26 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 118 
 HIS   0.002   0.001   HIS B 201 
 PHE   0.010   0.002   PHE A 219 
 TYR   0.013   0.001   TYR A 109 
 ARG   0.001   0.000   ARG A 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04369 (  316)
  hydrogen bonds       : angle       4.70185 (  936)
  SS BOND              : bond        0.00240 (    2)
  SS BOND              : angle       1.00353 (    4)
  covalent geometry    : bond        0.00324 ( 4060)
  covalent geometry    : angle       0.62215 ( 5526)
  Misc. bond           : bond        0.00146 (    4)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7605 (mt0)
REVERT: A  103 LYS cc_start: 0.7363 (mmtm) cc_final: 0.6708 (mtpt)
REVERT: A  194 LYS cc_start: 0.7452 (mtpt) cc_final: 0.6605 (mmtt)
REVERT: A  273 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6194 (tp30)
REVERT: B   56 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7614 (mt0)
REVERT: B  103 LYS cc_start: 0.7375 (mmtm) cc_final: 0.6719 (mtpt)
REVERT: B  194 LYS cc_start: 0.7123 (mmmt) cc_final: 0.6420 (mtpm)
REVERT: B  273 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6178 (tp30)
  outliers start: 11
  outliers final: 8
  residues processed: 57
  average time/residue: 1.1645
  time to fit residues: 68.8049
Evaluate side-chains
  61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 CYS
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   56 GLN
Chi-restraints excluded: chain B residue  100 PHE
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  276 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 30 optimal weight:    0.0980
   chunk 19 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
B  46 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.124728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.110229 restraints weight = 4172.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.43
r_work: 0.3172 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4066  Z= 0.152
  Angle     :  0.626  11.843   5530  Z= 0.322
  Chirality :  0.042   0.239    604
  Planarity :  0.009   0.152    668
  Dihedral  :  6.141  53.204    552
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.56 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.23 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    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:  2.09 (0.38), residues: 488
  helix:  2.31 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.22 (0.59), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 118 
 HIS   0.002   0.001   HIS B 201 
 PHE   0.010   0.002   PHE A 219 
 TYR   0.013   0.001   TYR A 109 
 ARG   0.001   0.000   ARG A 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 (  316)
  hydrogen bonds       : angle       4.67969 (  936)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       0.98848 (    4)
  covalent geometry    : bond        0.00318 ( 4060)
  covalent geometry    : angle       0.62522 ( 5526)
  Misc. bond           : bond        0.00141 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4646.70 seconds
wall clock time: 81 minutes 2.44 seconds (4862.44 seconds total)