Starting phenix.real_space_refine
on Wed Sep 17 03:17:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iqv_60796/09_2025/9iqv_60796.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iqv_60796/09_2025/9iqv_60796.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iqv_60796/09_2025/9iqv_60796.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iqv_60796/09_2025/9iqv_60796.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iqv_60796/09_2025/9iqv_60796.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iqv_60796/09_2025/9iqv_60796.map"
  }
  resolution = 3.3
  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=  -0.001 sd=   0.063
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      24      5.16       5
     C    1760      2.51       5
     N     429      2.21       5
     O     449      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 2662
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
    Chain: "B"
      Number of atoms: 2150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2150
          Classifications: {'peptide': 273}
          Link IDs: {'PTRANS': 14, 'TRANS': 258}
          Chain breaks: 1
  Time building chain proxies: 0.86, per 1000 atoms: 0.32
  Number of scatterers: 2662
  At special positions: 0
  Unit cell: (53.5, 73.83, 90.95, 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      24     16.00
     O     449      8.00
     N     429      7.00
     C    1760      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   3 " - pdb=" SG  CYS A  24 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  17 " - pdb=" SG  CYS A  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  46 " - pdb=" SG  CYS A  57 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  58 " - pdb=" SG  CYS A  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  99 " - pdb=" SG  CYS B 176 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 103.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  634

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 2 sheets defined
      71.0% alpha, 9.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'B' and resid 23 through 53
    Processing helix  chain 'B' and resid 59 through 90
      Proline residue:  B  81  - end of helix
    Processing helix  chain 'B' and resid 95 through 130
      removed outlier: 4.165A  pdb=" N   ILE B 114 " --> pdb=" O   CYS B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 138
    Processing helix  chain 'B' and resid 139 through 164
      Proline residue:  B 161  - end of helix
    Processing helix  chain 'B' and resid 181 through 214
      removed outlier: 3.698A  pdb=" N   VAL B 185 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   LEU B 195 " --> pdb=" O   GLY B 191 " (cutoff:3.500A)
      Proline residue:  B 196  - end of helix
    Processing helix  chain 'B' and resid 263 through 298
      Proline residue:  B 287  - end of helix
      Proline residue:  B 293  - end of helix
    Processing helix  chain 'B' and resid 304 through 330
      removed outlier: 3.581A  pdb=" N   PHE B 308 " --> pdb=" O   SER B 304 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASN B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
      Proline residue:  B 323  - end of helix
      Proline residue:  B 327  - end of helix
    Processing helix  chain 'B' and resid 330 through 341
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8
      removed outlier: 4.973A  pdb=" N   VAL A   4 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   GLU A  15 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LYS A   6 " --> pdb=" O   THR A  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 43
      removed outlier: 6.833A  pdb=" N   TYR A  35 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   VAL A  31 " --> pdb=" O   TYR A  35 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   CYS A  24 " --> pdb=" O   CYS A  58 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER A  54 " --> pdb=" O   TRP A  28 " (cutoff:3.500A)

    193 hydrogen bonds defined for protein.
    573 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: 0.25

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 802
        1.35 -     1.47: 691
        1.47 -     1.59: 1212
        1.59 -     1.71: 0
        1.71 -     1.83: 28
  Bond restraints: 2733
  Sorted by residual:
  bond pdb=" CB  MET B 203 "
       pdb=" CG  MET B 203 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" CB  ASN A  64 "
       pdb=" CG  ASN A  64 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 9.91e-01
  bond pdb=" CA  ASN A  64 "
       pdb=" CB  ASN A  64 "
    ideal  model  delta    sigma   weight residual
    1.535  1.548 -0.013 1.37e-02 5.33e+03 9.18e-01
  bond pdb=" CG  MET B 203 "
       pdb=" SD  MET B 203 "
    ideal  model  delta    sigma   weight residual
    1.803  1.782  0.021 2.50e-02 1.60e+03 7.14e-01
  bond pdb=" CG1 ILE B 175 "
       pdb=" CD1 ILE B 175 "
    ideal  model  delta    sigma   weight residual
    1.513  1.480  0.033 3.90e-02 6.57e+02 6.96e-01
  ... (remaining 2728 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 3505
        1.12 -     2.25: 159
        2.25 -     3.37: 38
        3.37 -     4.50: 15
        4.50 -     5.62: 7
  Bond angle restraints: 3724
  Sorted by residual:
  angle pdb=" C   ILE B 175 "
        pdb=" N   CYS B 176 "
        pdb=" CA  CYS B 176 "
      ideal   model   delta    sigma   weight residual
     123.25  119.46    3.79 1.69e+00 3.50e-01 5.04e+00
  angle pdb=" CA  ASN A  64 "
        pdb=" CB  ASN A  64 "
        pdb=" CG  ASN A  64 "
      ideal   model   delta    sigma   weight residual
     112.60  114.84   -2.24 1.00e+00 1.00e+00 5.00e+00
  angle pdb=" N   LYS A  59 "
        pdb=" CA  LYS A  59 "
        pdb=" C   LYS A  59 "
      ideal   model   delta    sigma   weight residual
     110.56  114.75   -4.19 1.94e+00 2.66e-01 4.66e+00
  angle pdb=" C   CYS A  63 "
        pdb=" N   ASN A  64 "
        pdb=" CA  ASN A  64 "
      ideal   model   delta    sigma   weight residual
     125.02  128.59   -3.57 1.76e+00 3.23e-01 4.12e+00
  angle pdb=" N   GLY B 160 "
        pdb=" CA  GLY B 160 "
        pdb=" C   GLY B 160 "
      ideal   model   delta    sigma   weight residual
     112.34  116.21   -3.87 2.04e+00 2.40e-01 3.60e+00
  ... (remaining 3719 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.66: 1363
       12.66 -    25.33: 176
       25.33 -    37.99: 54
       37.99 -    50.65: 14
       50.65 -    63.32: 5
  Dihedral angle restraints: 1612
    sinusoidal: 628
      harmonic: 984
  Sorted by residual:
  dihedral pdb=" CB  CYS A  58 "
           pdb=" SG  CYS A  58 "
           pdb=" SG  CYS A  63 "
           pdb=" CB  CYS A  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.37   52.37     1      1.00e+01 1.00e-02 3.74e+01
  dihedral pdb=" CA  VAL A  31 "
           pdb=" C   VAL A  31 "
           pdb=" N   ILE A  32 "
           pdb=" CA  ILE A  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.02  -17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  PHE B 193 "
           pdb=" C   PHE B 193 "
           pdb=" N   TYR B 194 "
           pdb=" CA  TYR B 194 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.29  -17.71     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 1609 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 278
       0.035 -    0.071: 113
       0.071 -    0.106: 27
       0.106 -    0.141: 16
       0.141 -    0.176: 3
  Chirality restraints: 437
  Sorted by residual:
  chirality pdb=" CA  TYR B 204 "
            pdb=" N   TYR B 204 "
            pdb=" C   TYR B 204 "
            pdb=" CB  TYR B 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.78e-01
  chirality pdb=" CB  ILE A  32 "
            pdb=" CA  ILE A  32 "
            pdb=" CG1 ILE A  32 "
            pdb=" CG2 ILE A  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.31e-01
  chirality pdb=" CA  ILE A  32 "
            pdb=" N   ILE A  32 "
            pdb=" C   ILE A  32 "
            pdb=" CB  ILE A  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.07e-01
  ... (remaining 434 not shown)

  Planarity restraints: 454
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  76 "    0.009 2.00e-02 2.50e+03   1.91e-02 3.67e+00
        pdb=" C   THR B  76 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   THR B  76 "    0.012 2.00e-02 2.50e+03
        pdb=" N   SER B  77 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  32 "   -0.031 5.00e-02 4.00e+02   4.62e-02 3.41e+00
        pdb=" N   PRO A  33 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A  33 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  33 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 204 "   -0.016 2.00e-02 2.50e+03   1.23e-02 3.03e+00
        pdb=" CG  TYR B 204 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 204 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 204 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 204 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 204 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 204 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 204 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 451 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 290
        2.75 -     3.28: 2774
        3.28 -     3.82: 4555
        3.82 -     4.36: 5069
        4.36 -     4.90: 8770
  Nonbonded interactions: 21458
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  61 "
            pdb=" OD2 ASP B 123 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG  SER A  54 "
            pdb=" OD2 ASP B 172 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" NH2 ARG A  40 "
            pdb=" O   CYS A  63 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" OH  TYR B 194 "
            pdb=" O   PHE B 289 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OD1 ASP B 123 "
            pdb=" OH  TYR B 134 "
     model   vdw
     2.360 3.040
  ... (remaining 21453 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.790
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
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   0.033   2738  Z= 0.156
  Angle     :  0.644   5.622   3734  Z= 0.344
  Chirality :  0.045   0.176    437
  Planarity :  0.005   0.046    454
  Dihedral  : 12.859  63.316    963
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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:  0.67 (0.48), residues: 332
  helix:  1.61 (0.35), residues: 223
  sheet: -1.95 (0.99), residues: 25
  loop : -2.01 (0.72), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  40 
 TYR   0.030   0.002   TYR B 204 
 PHE   0.013   0.001   PHE B  86 
 TRP   0.011   0.001   TRP B 313 
 HIS   0.002   0.001   HIS A  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 2733)
  covalent geometry    : angle       0.64265 ( 3724)
  SS BOND              : bond        0.00262 (    5)
  SS BOND              : angle       1.12446 (   10)
  hydrogen bonds       : bond        0.10338 (  193)
  hydrogen bonds       : angle       5.45892 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.060 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0451
  time to fit residues: 3.5198
Evaluate side-chains
  50 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.179292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.144533 restraints weight = 3562.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 2.39
r_work: 0.3697 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2738  Z= 0.161
  Angle     :  0.684   7.795   3734  Z= 0.347
  Chirality :  0.046   0.183    437
  Planarity :  0.005   0.046    454
  Dihedral  :  4.849  16.874    363
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.14 %
    Favored  : 88.18 %
  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:  0.83 (0.48), residues: 332
  helix:  1.75 (0.34), residues: 223
  sheet: -1.88 (0.99), residues: 25
  loop : -1.99 (0.73), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  40 
 TYR   0.012   0.002   TYR B 134 
 PHE   0.016   0.001   PHE B  86 
 TRP   0.009   0.001   TRP B 313 
 HIS   0.007   0.002   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 2733)
  covalent geometry    : angle       0.67473 ( 3724)
  SS BOND              : bond        0.00307 (    5)
  SS BOND              : angle       2.27801 (   10)
  hydrogen bonds       : bond        0.04390 (  193)
  hydrogen bonds       : angle       4.78675 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.080 
Fit side-chains
REVERT: B   41 VAL cc_start: 0.8855 (t) cc_final: 0.8641 (m)
REVERT: B   80 LEU cc_start: 0.8242 (mt) cc_final: 0.7931 (mt)
REVERT: B  301 PHE cc_start: 0.7580 (m-80) cc_final: 0.7354 (m-80)
REVERT: B  309 LYS cc_start: 0.7766 (mttm) cc_final: 0.7429 (mttm)
  outliers start: 5
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0560
  time to fit residues: 4.1295
Evaluate side-chains
  59 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain B residue   98 PHE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 0 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B  54 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.176989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.142017 restraints weight = 3598.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.38
r_work: 0.3669 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2738  Z= 0.177
  Angle     :  0.684   7.500   3734  Z= 0.349
  Chirality :  0.046   0.173    437
  Planarity :  0.005   0.045    454
  Dihedral  :  4.850  17.083    363
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 11.82 %
    Favored  : 84.46 %
  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:  0.71 (0.48), residues: 332
  helix:  1.64 (0.34), residues: 221
  sheet: -2.12 (0.98), residues: 25
  loop : -1.80 (0.71), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  40 
 TYR   0.012   0.002   TYR B 184 
 PHE   0.016   0.001   PHE B  86 
 TRP   0.007   0.001   TRP B 313 
 HIS   0.009   0.002   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 2733)
  covalent geometry    : angle       0.67598 ( 3724)
  SS BOND              : bond        0.00353 (    5)
  SS BOND              : angle       2.07191 (   10)
  hydrogen bonds       : bond        0.04488 (  193)
  hydrogen bonds       : angle       4.72475 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.103 
Fit side-chains
REVERT: B   41 VAL cc_start: 0.8895 (t) cc_final: 0.8674 (m)
REVERT: B   63 TYR cc_start: 0.7457 (m-80) cc_final: 0.7193 (m-80)
REVERT: B   98 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6795 (t80)
REVERT: B  181 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7374 (mm-30)
REVERT: B  194 TYR cc_start: 0.7269 (m-80) cc_final: 0.6937 (m-80)
REVERT: B  301 PHE cc_start: 0.7609 (m-80) cc_final: 0.7298 (m-80)
  outliers start: 11
  outliers final: 7
  residues processed: 62
  average time/residue: 0.0635
  time to fit residues: 4.7135
Evaluate side-chains
  60 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   98 PHE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 20 optimal weight:    0.4980
   chunk 6 optimal weight:    8.9990
   chunk 8 optimal weight:    0.5980
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.179937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.145000 restraints weight = 3541.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 2.45
r_work: 0.3705 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2738  Z= 0.138
  Angle     :  0.640   6.709   3734  Z= 0.328
  Chirality :  0.045   0.194    437
  Planarity :  0.005   0.055    454
  Dihedral  :  4.636  17.334    363
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.54 %
    Favored  : 82.09 %
  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:  0.98 (0.47), residues: 332
  helix:  1.81 (0.34), residues: 221
  sheet: -1.15 (1.52), residues: 14
  loop : -1.88 (0.63), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  40 
 TYR   0.011   0.001   TYR B 184 
 PHE   0.012   0.001   PHE B  86 
 TRP   0.009   0.001   TRP B 313 
 HIS   0.009   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 2733)
  covalent geometry    : angle       0.63527 ( 3724)
  SS BOND              : bond        0.00317 (    5)
  SS BOND              : angle       1.56894 (   10)
  hydrogen bonds       : bond        0.04145 (  193)
  hydrogen bonds       : angle       4.53170 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.155 
Fit side-chains
REVERT: B   41 VAL cc_start: 0.8872 (t) cc_final: 0.8639 (m)
REVERT: B   98 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6736 (t80)
REVERT: B  301 PHE cc_start: 0.7431 (m-80) cc_final: 0.7210 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 59
  average time/residue: 0.0657
  time to fit residues: 4.6565
Evaluate side-chains
  52 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain B residue   98 PHE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  318 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 30 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.178285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.144013 restraints weight = 3523.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 2.33
r_work: 0.3700 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2738  Z= 0.153
  Angle     :  0.660   6.991   3734  Z= 0.338
  Chirality :  0.046   0.200    437
  Planarity :  0.005   0.057    454
  Dihedral  :  4.666  18.189    363
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.23 %
    Favored  : 79.73 %
  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:  0.84 (0.47), residues: 332
  helix:  1.73 (0.34), residues: 221
  sheet: -2.15 (0.95), residues: 25
  loop : -1.69 (0.70), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 124 
 TYR   0.010   0.001   TYR B 134 
 PHE   0.015   0.001   PHE B  86 
 TRP   0.006   0.001   TRP B 313 
 HIS   0.009   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 2733)
  covalent geometry    : angle       0.65707 ( 3724)
  SS BOND              : bond        0.00267 (    5)
  SS BOND              : angle       1.41440 (   10)
  hydrogen bonds       : bond        0.04299 (  193)
  hydrogen bonds       : angle       4.54060 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: B   98 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6832 (t80)
REVERT: B  181 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7032 (mm-30)
REVERT: B  301 PHE cc_start: 0.7334 (m-80) cc_final: 0.7122 (m-80)
  outliers start: 9
  outliers final: 6
  residues processed: 59
  average time/residue: 0.0717
  time to fit residues: 5.0860
Evaluate side-chains
  58 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   98 PHE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.177368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.142683 restraints weight = 3554.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 2.37
r_work: 0.3686 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2738  Z= 0.160
  Angle     :  0.656   6.834   3734  Z= 0.338
  Chirality :  0.046   0.178    437
  Planarity :  0.005   0.056    454
  Dihedral  :  4.705  17.864    363
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.26 %
    Favored  : 77.36 %
  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:  0.92 (0.47), residues: 332
  helix:  1.71 (0.34), residues: 221
  sheet: -1.23 (1.51), residues: 14
  loop : -1.74 (0.64), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 124 
 TYR   0.009   0.001   TYR B 134 
 PHE   0.015   0.001   PHE B  86 
 TRP   0.006   0.001   TRP B 313 
 HIS   0.009   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 2733)
  covalent geometry    : angle       0.65111 ( 3724)
  SS BOND              : bond        0.00294 (    5)
  SS BOND              : angle       1.60402 (   10)
  hydrogen bonds       : bond        0.04322 (  193)
  hydrogen bonds       : angle       4.59404 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.108 
Fit side-chains
REVERT: B   63 TYR cc_start: 0.7315 (m-80) cc_final: 0.7048 (m-80)
REVERT: B   98 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6764 (t80)
REVERT: B  301 PHE cc_start: 0.7375 (m-80) cc_final: 0.7168 (m-80)
REVERT: B  309 LYS cc_start: 0.7661 (mttm) cc_final: 0.7369 (mttm)
  outliers start: 10
  outliers final: 5
  residues processed: 63
  average time/residue: 0.0659
  time to fit residues: 4.9477
Evaluate side-chains
  62 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   98 PHE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   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  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.177875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.143487 restraints weight = 3520.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 2.33
r_work: 0.3699 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2738  Z= 0.154
  Angle     :  0.672   7.286   3734  Z= 0.345
  Chirality :  0.046   0.204    437
  Planarity :  0.005   0.058    454
  Dihedral  :  4.709  17.797    363
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 20.27 %
    Favored  : 76.35 %
  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:  0.82 (0.46), residues: 332
  helix:  1.58 (0.34), residues: 222
  sheet: -1.22 (1.47), residues: 14
  loop : -1.67 (0.64), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 124 
 TYR   0.012   0.001   TYR B 125 
 PHE   0.016   0.001   PHE B  39 
 TRP   0.006   0.001   TRP A  28 
 HIS   0.009   0.002   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 2733)
  covalent geometry    : angle       0.66848 ( 3724)
  SS BOND              : bond        0.00276 (    5)
  SS BOND              : angle       1.42200 (   10)
  hydrogen bonds       : bond        0.04315 (  193)
  hydrogen bonds       : angle       4.54056 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.104 
Fit side-chains
REVERT: B   74 LEU cc_start: 0.7676 (tt) cc_final: 0.6996 (tp)
REVERT: B   98 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6788 (t80)
REVERT: B  309 LYS cc_start: 0.7648 (mttm) cc_final: 0.7342 (mttm)
  outliers start: 10
  outliers final: 5
  residues processed: 60
  average time/residue: 0.0707
  time to fit residues: 5.0639
Evaluate side-chains
  56 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   98 PHE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.177348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.142867 restraints weight = 3589.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.34
r_work: 0.3691 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2738  Z= 0.161
  Angle     :  0.696   6.866   3734  Z= 0.358
  Chirality :  0.047   0.193    437
  Planarity :  0.005   0.057    454
  Dihedral  :  4.765  18.197    363
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.96 %
    Favored  : 75.34 %
  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:  0.89 (0.47), residues: 332
  helix:  1.66 (0.34), residues: 222
  sheet: -1.20 (1.49), residues: 14
  loop : -1.72 (0.64), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 124 
 TYR   0.012   0.002   TYR B 125 
 PHE   0.014   0.001   PHE B  86 
 TRP   0.006   0.001   TRP B 313 
 HIS   0.009   0.002   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 2733)
  covalent geometry    : angle       0.69353 ( 3724)
  SS BOND              : bond        0.00278 (    5)
  SS BOND              : angle       1.39475 (   10)
  hydrogen bonds       : bond        0.04361 (  193)
  hydrogen bonds       : angle       4.55323 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.107 
Fit side-chains
REVERT: B   74 LEU cc_start: 0.7625 (tt) cc_final: 0.6941 (tp)
REVERT: B   98 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6764 (t80)
REVERT: B  181 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6975 (mm-30)
REVERT: B  194 TYR cc_start: 0.7078 (m-80) cc_final: 0.6788 (m-80)
REVERT: B  309 LYS cc_start: 0.7628 (mttm) cc_final: 0.7341 (mttm)
  outliers start: 8
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0742
  time to fit residues: 4.9153
Evaluate side-chains
  58 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   98 PHE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 4 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0970
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.178189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.143914 restraints weight = 3612.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 2.32
r_work: 0.3705 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2738  Z= 0.151
  Angle     :  0.698   7.192   3734  Z= 0.359
  Chirality :  0.047   0.192    437
  Planarity :  0.005   0.056    454
  Dihedral  :  4.764  19.333    363
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 21.62 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.96 (0.47), residues: 332
  helix:  1.71 (0.34), residues: 222
  sheet: -1.12 (1.48), residues: 14
  loop : -1.69 (0.64), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 124 
 TYR   0.011   0.001   TYR B 125 
 PHE   0.026   0.002   PHE B 301 
 TRP   0.007   0.001   TRP B 313 
 HIS   0.009   0.002   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 2733)
  covalent geometry    : angle       0.69555 ( 3724)
  SS BOND              : bond        0.00276 (    5)
  SS BOND              : angle       1.29169 (   10)
  hydrogen bonds       : bond        0.04283 (  193)
  hydrogen bonds       : angle       4.50188 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.104 
Fit side-chains
REVERT: B   74 LEU cc_start: 0.7679 (tt) cc_final: 0.7105 (tp)
REVERT: B   98 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6761 (t80)
REVERT: B  181 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6968 (mm-30)
  outliers start: 7
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0730
  time to fit residues: 4.7981
Evaluate side-chains
  54 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   98 PHE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    0.1980
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0020
   chunk 31 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  56 HIS
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.178671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.144747 restraints weight = 3599.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 2.33
r_work: 0.3724 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2738  Z= 0.146
  Angle     :  0.697   7.145   3734  Z= 0.361
  Chirality :  0.047   0.181    437
  Planarity :  0.005   0.057    454
  Dihedral  :  4.734  21.197    363
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.30 %
    Favored  : 75.34 %
  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:  1.05 (0.47), residues: 332
  helix:  1.80 (0.34), residues: 224
  sheet: -1.06 (1.47), residues: 14
  loop : -1.82 (0.64), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 124 
 TYR   0.010   0.001   TYR B 125 
 PHE   0.028   0.002   PHE B 301 
 TRP   0.007   0.001   TRP B 313 
 HIS   0.007   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 2733)
  covalent geometry    : angle       0.69410 ( 3724)
  SS BOND              : bond        0.00279 (    5)
  SS BOND              : angle       1.37219 (   10)
  hydrogen bonds       : bond        0.04207 (  193)
  hydrogen bonds       : angle       4.43310 (  573)

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

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

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  664 Ramachandran restraints generated.
    332 Oldfield, 0 Emsley, 332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.106 
Fit side-chains
REVERT: B   74 LEU cc_start: 0.7665 (tt) cc_final: 0.7127 (tp)
REVERT: B   98 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6806 (t80)
REVERT: B  125 TYR cc_start: 0.7634 (t80) cc_final: 0.7324 (t80)
REVERT: B  181 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6992 (mm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0701
  time to fit residues: 4.6400
Evaluate side-chains
  60 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   56 HIS
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   98 PHE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 31 optimal weight:    0.1980
   chunk 29 optimal weight:    0.0040
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0870
   chunk 5 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.3570

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

Flipped N/Q/H residues before XYZ refinement:
A  56 HIS
B  54 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.180224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.146736 restraints weight = 3557.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 2.30
r_work: 0.3759 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2738  Z= 0.140
  Angle     :  0.684   7.151   3734  Z= 0.357
  Chirality :  0.047   0.190    437
  Planarity :  0.005   0.058    454
  Dihedral  :  4.690  20.722    363
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 21.62 %
    Favored  : 75.34 %
  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:  1.08 (0.47), residues: 332
  helix:  1.82 (0.34), residues: 224
  sheet: -1.09 (1.41), residues: 14
  loop : -1.78 (0.64), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 124 
 TYR   0.010   0.001   TYR B 125 
 PHE   0.028   0.001   PHE B 301 
 TRP   0.008   0.001   TRP B 313 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 2733)
  covalent geometry    : angle       0.68178 ( 3724)
  SS BOND              : bond        0.00255 (    5)
  SS BOND              : angle       1.35715 (   10)
  hydrogen bonds       : bond        0.04062 (  193)
  hydrogen bonds       : angle       4.40035 (  573)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 792.36 seconds
wall clock time: 14 minutes 21.25 seconds (861.25 seconds total)