Starting phenix.real_space_refine
on Wed Sep 17 04:14:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zan_39881/09_2025/8zan_39881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zan_39881/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zan_39881/09_2025/8zan_39881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zan_39881/09_2025/8zan_39881.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zan_39881/09_2025/8zan_39881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zan_39881/09_2025/8zan_39881.map"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.01, per 1000 atoms: 0.26
  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: 0.36
  Conformation dependent library (CDL) restraints added in 145.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.08
  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: 0.55

  Time building geometry restraints manager: 0.43 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: 0.01
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:             25.110
  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:          0.260
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.280
  Find NCS groups from input model:        0.040
  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:7.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.550
-------------------------------------------------------------------------------
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 : 9.32
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 120 
 TYR   0.011   0.001   TYR A 109 
 PHE   0.010   0.002   PHE B 178 
 TRP   0.009   0.001   TRP A  75 
 HIS   0.002   0.001   HIS B 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4060)
  covalent geometry    : angle       0.65013 ( 5526)
  SS BOND              : bond        0.00297 (    2)
  SS BOND              : angle       1.04719 (    4)
  hydrogen bonds       : bond        0.11505 (  316)
  hydrogen bonds       : angle       5.26418 (  936)
  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  : 0.156 
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: 0.6630
  time to fit residues: 38.2296
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  : 0.146 
-------------------------------------------------------------------------------
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 24 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.123188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.107802 restraints weight = 4239.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.56
r_work: 0.3171 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.0723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4066  Z= 0.195
  Angle     :  0.633   8.794   5530  Z= 0.341
  Chirality :  0.044   0.246    604
  Planarity :  0.009   0.144    668
  Dihedral  :  7.363  51.182    574
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  5.33 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.39), residues: 488
  helix:  2.07 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.35 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 209 
 TYR   0.015   0.001   TYR A 109 
 PHE   0.012   0.002   PHE B 178 
 TRP   0.010   0.001   TRP B  75 
 HIS   0.003   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 4060)
  covalent geometry    : angle       0.63341 ( 5526)
  SS BOND              : bond        0.00192 (    2)
  SS BOND              : angle       0.60324 (    4)
  hydrogen bonds       : bond        0.04814 (  316)
  hydrogen bonds       : angle       4.82776 (  936)
  Misc. bond           : bond        0.00208 (    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  : 0.096 
Fit side-chains
REVERT: A  103 LYS cc_start: 0.7557 (mmtm) cc_final: 0.6879 (mtpt)
REVERT: A  194 LYS cc_start: 0.7761 (mtpt) cc_final: 0.6963 (mmtt)
REVERT: A  273 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6369 (tp30)
REVERT: B  103 LYS cc_start: 0.7550 (mmtm) cc_final: 0.6867 (mtpt)
REVERT: B  194 LYS cc_start: 0.7444 (mmmt) cc_final: 0.6783 (mtpm)
REVERT: B  273 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6347 (tp30)
  outliers start: 6
  outliers final: 4
  residues processed: 57
  average time/residue: 0.6850
  time to fit residues: 40.1188
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  : 0.190 
-------------------------------------------------------------------------------
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 28 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.123077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.108377 restraints weight = 4203.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.45
r_work: 0.3151 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4066  Z= 0.176
  Angle     :  0.609   8.898   5530  Z= 0.326
  Chirality :  0.043   0.246    604
  Planarity :  0.009   0.144    668
  Dihedral  :  6.466  53.100    554
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  6.56 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.47 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.38), residues: 488
  helix:  2.12 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.35 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 268 
 TYR   0.015   0.001   TYR A 109 
 PHE   0.011   0.002   PHE A 178 
 TRP   0.007   0.001   TRP A 118 
 HIS   0.002   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 4060)
  covalent geometry    : angle       0.60854 ( 5526)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       0.67939 (    4)
  hydrogen bonds       : bond        0.04636 (  316)
  hydrogen bonds       : angle       4.80404 (  936)
  Misc. bond           : bond        0.00185 (    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  : 0.158 
Fit side-chains
REVERT: A  103 LYS cc_start: 0.7203 (mmtm) cc_final: 0.6526 (mtpt)
REVERT: A  194 LYS cc_start: 0.7433 (mtpt) cc_final: 0.6574 (mmtt)
REVERT: A  273 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6156 (tp30)
REVERT: B  103 LYS cc_start: 0.7204 (mmtm) cc_final: 0.6525 (mtpt)
REVERT: B  194 LYS cc_start: 0.7110 (mmmt) cc_final: 0.6402 (mtpm)
REVERT: B  273 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6117 (tp30)
  outliers start: 10
  outliers final: 2
  residues processed: 58
  average time/residue: 0.6963
  time to fit residues: 41.5464
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  : 0.154 
-------------------------------------------------------------------------------
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 44 optimal weight:    0.0050
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.5994

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.124839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.109855 restraints weight = 4155.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.47
r_work: 0.3171 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.0911

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     :  0.585   8.533   5530  Z= 0.313
  Chirality :  0.042   0.248    604
  Planarity :  0.008   0.143    668
  Dihedral  :  6.337  54.006    554
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  6.56 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.38), residues: 488
  helix:  2.19 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.36 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 147 
 TYR   0.013   0.001   TYR B 109 
 PHE   0.010   0.002   PHE A 178 
 TRP   0.007   0.001   TRP B 118 
 HIS   0.002   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4060)
  covalent geometry    : angle       0.58503 ( 5526)
  SS BOND              : bond        0.00067 (    2)
  SS BOND              : angle       0.56727 (    4)
  hydrogen bonds       : bond        0.04402 (  316)
  hydrogen bonds       : angle       4.71005 (  936)
  Misc. bond           : bond        0.00147 (    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  : 0.096 
Fit side-chains
REVERT: A  103 LYS cc_start: 0.7155 (mmtm) cc_final: 0.6496 (mtpt)
REVERT: A  194 LYS cc_start: 0.7403 (mtpt) cc_final: 0.6543 (mmtt)
REVERT: A  273 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6130 (tp30)
REVERT: B  103 LYS cc_start: 0.7159 (mmtm) cc_final: 0.6496 (mtpt)
REVERT: B  194 LYS cc_start: 0.7070 (mmmt) cc_final: 0.6371 (mtpm)
REVERT: B  273 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6103 (tp30)
  outliers start: 8
  outliers final: 0
  residues processed: 62
  average time/residue: 0.6423
  time to fit residues: 40.8924
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  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 20 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3466 r_free = 0.3466 target = 0.125299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.110325 restraints weight = 4192.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.49
r_work: 0.3172 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4066  Z= 0.158
  Angle     :  0.588   8.444   5530  Z= 0.313
  Chirality :  0.042   0.247    604
  Planarity :  0.008   0.143    668
  Dihedral  :  6.118  53.159    552
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.97 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.39), residues: 488
  helix:  2.22 (0.26), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.47 (0.56), residues: 110

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4060)
  covalent geometry    : angle       0.58488 ( 5526)
  SS BOND              : bond        0.00556 (    2)
  SS BOND              : angle       2.17060 (    4)
  hydrogen bonds       : bond        0.04363 (  316)
  hydrogen bonds       : angle       4.73271 (  936)
  Misc. bond           : bond        0.00147 (    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
  64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7602 (mt0)
REVERT: A  103 LYS cc_start: 0.7198 (mmtm) cc_final: 0.6536 (mtpt)
REVERT: A  194 LYS cc_start: 0.7414 (mtpt) cc_final: 0.6559 (mmtt)
REVERT: A  273 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6145 (tp30)
REVERT: B   56 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7606 (mt0)
REVERT: B  103 LYS cc_start: 0.7208 (mmtm) cc_final: 0.6539 (mtpt)
REVERT: B  194 LYS cc_start: 0.7089 (mmmt) cc_final: 0.6388 (mtpm)
REVERT: B  273 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6116 (tp30)
  outliers start: 11
  outliers final: 5
  residues processed: 58
  average time/residue: 0.6452
  time to fit residues: 38.5325
Evaluate side-chains
  60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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  276 LEU
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   56 GLN
Chi-restraints excluded: chain B residue  139 THR
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 13 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.124587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.109513 restraints weight = 4218.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.50
r_work: 0.3165 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4066  Z= 0.160
  Angle     :  0.598   9.519   5530  Z= 0.316
  Chirality :  0.042   0.240    604
  Planarity :  0.009   0.146    668
  Dihedral  :  6.135  52.289    552
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.97 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.39), residues: 488
  helix:  2.19 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.41 (0.57), residues: 108

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4060)
  covalent geometry    : angle       0.59749 ( 5526)
  SS BOND              : bond        0.00366 (    2)
  SS BOND              : angle       1.41713 (    4)
  hydrogen bonds       : bond        0.04399 (  316)
  hydrogen bonds       : angle       4.72098 (  936)
  Misc. bond           : bond        0.00156 (    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
  68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7528 (mt0)
REVERT: A  103 LYS cc_start: 0.7192 (mmtm) cc_final: 0.6552 (mtpt)
REVERT: A  194 LYS cc_start: 0.7403 (mtpt) cc_final: 0.6547 (mmtt)
REVERT: A  273 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6122 (tp30)
REVERT: B   56 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7536 (mt0)
REVERT: B  103 LYS cc_start: 0.7200 (mmtm) cc_final: 0.6554 (mtpt)
REVERT: B  194 LYS cc_start: 0.7067 (mmmt) cc_final: 0.6356 (mtpm)
REVERT: B  273 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6101 (tp30)
  outliers start: 13
  outliers final: 5
  residues processed: 62
  average time/residue: 0.6168
  time to fit residues: 39.3917
Evaluate side-chains
  59 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.123756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.108561 restraints weight = 4271.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 1.51
r_work: 0.3151 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4066  Z= 0.167
  Angle     :  0.627  11.316   5530  Z= 0.326
  Chirality :  0.042   0.225    604
  Planarity :  0.009   0.151    668
  Dihedral  :  6.197  51.570    552
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.97 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.24 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 20.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG A 268 
 TYR   0.014   0.001   TYR B 109 
 PHE   0.011   0.002   PHE A 178 
 TRP   0.007   0.001   TRP A 118 
 HIS   0.002   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 4060)
  covalent geometry    : angle       0.62588 ( 5526)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       1.29989 (    4)
  hydrogen bonds       : bond        0.04467 (  316)
  hydrogen bonds       : angle       4.74024 (  936)
  Misc. bond           : bond        0.00168 (    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
  64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7566 (mt0)
REVERT: A  103 LYS cc_start: 0.7240 (mmtm) cc_final: 0.6612 (mtpt)
REVERT: A  194 LYS cc_start: 0.7410 (mtpt) cc_final: 0.6552 (mmtt)
REVERT: A  273 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6137 (tp30)
REVERT: B   56 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7570 (mt0)
REVERT: B  103 LYS cc_start: 0.7235 (mmtm) cc_final: 0.6605 (mtpt)
REVERT: B  194 LYS cc_start: 0.7077 (mmmt) cc_final: 0.6361 (mtpm)
REVERT: B  273 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6114 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 58
  average time/residue: 0.6875
  time to fit residues: 41.0909
Evaluate side-chains
  62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
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 18 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   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 = 0.3453 r_free = 0.3453 target = 0.124092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.109034 restraints weight = 4189.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.49
r_work: 0.3160 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1093

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= 0.161
  Angle     :  0.622  11.718   5530  Z= 0.321
  Chirality :  0.042   0.232    604
  Planarity :  0.009   0.152    668
  Dihedral  :  6.194  52.406    552
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 7.92
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.38), residues: 488
  helix:  2.21 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.33 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 147 
 TYR   0.013   0.001   TYR B 109 
 PHE   0.010   0.002   PHE B 178 
 TRP   0.007   0.001   TRP A 118 
 HIS   0.002   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4060)
  covalent geometry    : angle       0.62147 ( 5526)
  SS BOND              : bond        0.00226 (    2)
  SS BOND              : angle       1.08464 (    4)
  hydrogen bonds       : bond        0.04421 (  316)
  hydrogen bonds       : angle       4.72371 (  936)
  Misc. bond           : bond        0.00159 (    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
  65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7575 (mt0)
REVERT: A  103 LYS cc_start: 0.7291 (mmtm) cc_final: 0.6641 (mtpt)
REVERT: A  194 LYS cc_start: 0.7421 (mtpt) cc_final: 0.6565 (mmtt)
REVERT: A  273 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6151 (tp30)
REVERT: B   56 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7582 (mt0)
REVERT: B  103 LYS cc_start: 0.7286 (mmtm) cc_final: 0.6632 (mtpt)
REVERT: B  194 LYS cc_start: 0.7096 (mmmt) cc_final: 0.6379 (mtpm)
REVERT: B  273 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6131 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 59
  average time/residue: 0.6721
  time to fit residues: 40.8278
Evaluate side-chains
  60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   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
B  46 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.123885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.108803 restraints weight = 4237.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.50
r_work: 0.3155 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
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   0.022   4066  Z= 0.163
  Angle     :  0.626  12.001   5530  Z= 0.322
  Chirality :  0.042   0.234    604
  Planarity :  0.009   0.153    668
  Dihedral  :  6.187  52.080    552
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 7.92
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.38), residues: 488
  helix:  2.22 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.33 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 147 
 TYR   0.014   0.001   TYR B 109 
 PHE   0.011   0.002   PHE B 178 
 TRP   0.007   0.001   TRP A 118 
 HIS   0.002   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4060)
  covalent geometry    : angle       0.62569 ( 5526)
  SS BOND              : bond        0.00252 (    2)
  SS BOND              : angle       1.08072 (    4)
  hydrogen bonds       : bond        0.04442 (  316)
  hydrogen bonds       : angle       4.72538 (  936)
  Misc. bond           : bond        0.00162 (    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  : 0.122 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7567 (mt0)
REVERT: A  103 LYS cc_start: 0.7309 (mmtm) cc_final: 0.6651 (mtpt)
REVERT: A  194 LYS cc_start: 0.7409 (mtpt) cc_final: 0.6550 (mmtt)
REVERT: A  273 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6138 (tp30)
REVERT: B   56 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7572 (mt0)
REVERT: B  103 LYS cc_start: 0.7303 (mmtm) cc_final: 0.6639 (mtpt)
REVERT: B  194 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6364 (mtpm)
REVERT: B  273 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6116 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 57
  average time/residue: 0.6002
  time to fit residues: 35.2903
Evaluate side-chains
  60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
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 31 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0770
   chunk 17 optimal weight:    0.0970
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.4936

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.126133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.111280 restraints weight = 4256.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.47
r_work: 0.3183 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1173

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= 0.142
  Angle     :  0.607  11.968   5530  Z= 0.311
  Chirality :  0.041   0.238    604
  Planarity :  0.009   0.153    668
  Dihedral  :  6.136  54.180    552
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.56 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.47 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.39), residues: 488
  helix:  2.30 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.27 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 147 
 TYR   0.012   0.001   TYR B 109 
 PHE   0.010   0.001   PHE A 219 
 TRP   0.007   0.001   TRP A 118 
 HIS   0.002   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4060)
  covalent geometry    : angle       0.60648 ( 5526)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       0.87789 (    4)
  hydrogen bonds       : bond        0.04236 (  316)
  hydrogen bonds       : angle       4.66216 (  936)
  Misc. bond           : bond        0.00126 (    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
  68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   56 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7531 (mt0)
REVERT: A  103 LYS cc_start: 0.7327 (mmtm) cc_final: 0.6668 (mtpt)
REVERT: A  194 LYS cc_start: 0.7404 (mtpt) cc_final: 0.6539 (mmtt)
REVERT: A  273 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6138 (tp30)
REVERT: B   56 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7530 (mt0)
REVERT: B  103 LYS cc_start: 0.7329 (mmtm) cc_final: 0.6668 (mtpt)
REVERT: B  194 LYS cc_start: 0.7032 (mmmt) cc_final: 0.6433 (mmtt)
REVERT: B  273 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6131 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 62
  average time/residue: 0.5369
  time to fit residues: 34.4991
Evaluate side-chains
  60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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 39 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0030
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7592

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.123709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.108875 restraints weight = 4237.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.48
r_work: 0.3152 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4066  Z= 0.166
  Angle     :  0.632  12.235   5530  Z= 0.324
  Chirality :  0.042   0.237    604
  Planarity :  0.009   0.153    668
  Dihedral  :  6.118  51.052    552
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.92
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.38), residues: 488
  helix:  2.26 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.27 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 268 
 TYR   0.014   0.001   TYR B 109 
 PHE   0.011   0.002   PHE A 178 
 TRP   0.007   0.001   TRP B 118 
 HIS   0.003   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4060)
  covalent geometry    : angle       0.63109 ( 5526)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       1.06639 (    4)
  hydrogen bonds       : bond        0.04434 (  316)
  hydrogen bonds       : angle       4.70852 (  936)
  Misc. bond           : bond        0.00164 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2525.90 seconds
wall clock time: 44 minutes 0.25 seconds (2640.25 seconds total)