Starting phenix.real_space_refine
on Tue Feb  3 12:20:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j4f_61134/02_2026/9j4f_61134.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j4f_61134/02_2026/9j4f_61134.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j4f_61134/02_2026/9j4f_61134.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j4f_61134/02_2026/9j4f_61134.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j4f_61134/02_2026/9j4f_61134.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j4f_61134/02_2026/9j4f_61134.map"
  }
  resolution = 2.49
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    1080      2.51       5
     N     318      2.21       5
     O     318      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1734
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 289
          Classifications: {'peptide': 36}
          Link IDs: {'TRANS': 35}
  Restraints were copied for chains:
    B, C, E, D, F
  Time building chain proxies: 0.37, per 1000 atoms: 0.21
  Number of scatterers: 1734
  At special positions: 0
  Unit cell: (75.53, 83.83, 32.37, 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      18     16.00
     O     318      8.00
     N     318      7.00
     C    1080      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  80 " - pdb=" SG  CYS A  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  80 " - pdb=" SG  CYS B  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  80 " - pdb=" SG  CYS C  83 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  80 " - pdb=" SG  CYS E  83 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  80 " - pdb=" SG  CYS D  83 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F  80 " - pdb=" SG  CYS F  83 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.07
  Conformation dependent library (CDL) restraints added in 48.5 milliseconds
  

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  408

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 30.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 71 through 73
      removed outlier: 6.616A  pdb=" N   MET A  71 " --> pdb=" O   HIS C  72 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 78 through 81
      removed outlier: 6.391A  pdb=" N   LYS A  78 " --> pdb=" O   LEU D  79 " (cutoff:3.500A)
      removed outlier: 8.509A  pdb=" N   LYS D  81 " --> pdb=" O   LYS A  78 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   CYS A  80 " --> pdb=" O   LYS D  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85
      removed outlier: 6.413A  pdb=" N   GLN A  84 " --> pdb=" O   VAL C  85 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 90 through 94
      removed outlier: 6.209A  pdb=" N   ASN A  90 " --> pdb=" O   VAL D  91 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   VAL D  93 " --> pdb=" O   ASN A  90 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   THR A  92 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 102 through 103
      removed outlier: 6.391A  pdb=" N   LYS A 102 " --> pdb=" O   ILE C 103 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 71 through 73
      removed outlier: 6.596A  pdb=" N   MET B  71 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 78 through 81
      removed outlier: 6.406A  pdb=" N   LYS B  78 " --> pdb=" O   LEU F  79 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   LYS F  81 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   CYS B  80 " --> pdb=" O   LYS F  81 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 84 through 85
      removed outlier: 6.422A  pdb=" N   GLN B  84 " --> pdb=" O   VAL E  85 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 94
      removed outlier: 6.238A  pdb=" N   ASN B  90 " --> pdb=" O   VAL F  91 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   VAL F  93 " --> pdb=" O   ASN B  90 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   THR B  92 " --> pdb=" O   VAL F  93 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 102 through 103
      removed outlier: 6.371A  pdb=" N   LYS B 102 " --> pdb=" O   ILE E 103 " (cutoff:3.500A)

    22 hydrogen bonds defined for protein.
    66 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: 0.21

  Time building geometry restraints manager: 0.12 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 529
        1.33 -     1.45: 190
        1.45 -     1.56: 1009
        1.56 -     1.68: 0
        1.68 -     1.80: 24
  Bond restraints: 1752
  Sorted by residual:
  bond pdb=" CB  CYS C  83 "
       pdb=" SG  CYS C  83 "
    ideal  model  delta    sigma   weight residual
    1.808  1.760  0.048 3.30e-02 9.18e+02 2.12e+00
  bond pdb=" CB  CYS E  83 "
       pdb=" SG  CYS E  83 "
    ideal  model  delta    sigma   weight residual
    1.808  1.760  0.048 3.30e-02 9.18e+02 2.11e+00
  bond pdb=" CB  CYS A  83 "
       pdb=" SG  CYS A  83 "
    ideal  model  delta    sigma   weight residual
    1.808  1.760  0.048 3.30e-02 9.18e+02 2.08e+00
  bond pdb=" CB  CYS B  83 "
       pdb=" SG  CYS B  83 "
    ideal  model  delta    sigma   weight residual
    1.808  1.761  0.047 3.30e-02 9.18e+02 2.06e+00
  bond pdb=" CB  CYS F  83 "
       pdb=" SG  CYS F  83 "
    ideal  model  delta    sigma   weight residual
    1.808  1.761  0.047 3.30e-02 9.18e+02 2.05e+00
  ... (remaining 1747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 2046
        1.13 -     2.27: 216
        2.27 -     3.40: 72
        3.40 -     4.54: 0
        4.54 -     5.67: 6
  Bond angle restraints: 2340
  Sorted by residual:
  angle pdb=" CG1 ILE C  86 "
        pdb=" CB  ILE C  86 "
        pdb=" CG2 ILE C  86 "
      ideal   model   delta    sigma   weight residual
     110.70  105.03    5.67 3.00e+00 1.11e-01 3.57e+00
  angle pdb=" CG1 ILE A  86 "
        pdb=" CB  ILE A  86 "
        pdb=" CG2 ILE A  86 "
      ideal   model   delta    sigma   weight residual
     110.70  105.05    5.65 3.00e+00 1.11e-01 3.55e+00
  angle pdb=" CG1 ILE E  86 "
        pdb=" CB  ILE E  86 "
        pdb=" CG2 ILE E  86 "
      ideal   model   delta    sigma   weight residual
     110.70  105.06    5.64 3.00e+00 1.11e-01 3.54e+00
  angle pdb=" CG1 ILE F  86 "
        pdb=" CB  ILE F  86 "
        pdb=" CG2 ILE F  86 "
      ideal   model   delta    sigma   weight residual
     110.70  105.07    5.63 3.00e+00 1.11e-01 3.53e+00
  angle pdb=" CG1 ILE B  86 "
        pdb=" CB  ILE B  86 "
        pdb=" CG2 ILE B  86 "
      ideal   model   delta    sigma   weight residual
     110.70  105.09    5.61 3.00e+00 1.11e-01 3.50e+00
  ... (remaining 2335 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.92: 839
        8.92 -    17.84: 169
       17.84 -    26.75: 36
       26.75 -    35.67: 36
       35.67 -    44.59: 12
  Dihedral angle restraints: 1092
    sinusoidal: 474
      harmonic: 618
  Sorted by residual:
  dihedral pdb=" CA  LYS C  74 "
           pdb=" C   LYS C  74 "
           pdb=" N   ASN C  75 "
           pdb=" CA  ASN C  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.12  -27.88     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" CA  LYS B  74 "
           pdb=" C   LYS B  74 "
           pdb=" N   ASN B  75 "
           pdb=" CA  ASN B  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.15  -27.85     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" CA  LYS F  74 "
           pdb=" C   LYS F  74 "
           pdb=" N   ASN F  75 "
           pdb=" CA  ASN F  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.16  -27.84     0      5.00e+00 4.00e-02 3.10e+01
  ... (remaining 1089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 64
       0.028 -    0.055: 102
       0.055 -    0.082: 56
       0.082 -    0.109: 24
       0.109 -    0.136: 24
  Chirality restraints: 270
  Sorted by residual:
  chirality pdb=" CA  ILE D  98 "
            pdb=" N   ILE D  98 "
            pdb=" C   ILE D  98 "
            pdb=" CB  ILE D  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  ILE E  98 "
            pdb=" N   ILE E  98 "
            pdb=" C   ILE E  98 "
            pdb=" CB  ILE E  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  ILE F  98 "
            pdb=" N   ILE F  98 "
            pdb=" C   ILE F  98 "
            pdb=" CB  ILE F  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 267 not shown)

  Planarity restraints: 288
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  86 "   -0.006 2.00e-02 2.50e+03   1.16e-02 1.34e+00
        pdb=" C   ILE A  86 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ILE A  86 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ASP A  87 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D  86 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.30e+00
        pdb=" C   ILE D  86 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ILE D  86 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASP D  87 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C  86 "   -0.006 2.00e-02 2.50e+03   1.12e-02 1.26e+00
        pdb=" C   ILE C  86 "    0.019 2.00e-02 2.50e+03
        pdb=" O   ILE C  86 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASP C  87 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 285 not shown)

  Histogram of nonbonded interaction distances:
        2.62 -     3.07: 1186
        3.07 -     3.53: 1630
        3.53 -     3.99: 2493
        3.99 -     4.44: 3117
        4.44 -     4.90: 5710
  Nonbonded interactions: 14136
  Sorted by model distance:
  nonbonded pdb=" N   LYS C  74 "
            pdb=" O   LYS C  74 "
     model   vdw
     2.616 2.496
  nonbonded pdb=" N   LYS D  74 "
            pdb=" O   LYS D  74 "
     model   vdw
     2.616 2.496
  nonbonded pdb=" N   LYS A  74 "
            pdb=" O   LYS A  74 "
     model   vdw
     2.617 2.496
  nonbonded pdb=" N   LYS E  74 "
            pdb=" O   LYS E  74 "
     model   vdw
     2.617 2.496
  nonbonded pdb=" N   LYS B  74 "
            pdb=" O   LYS B  74 "
     model   vdw
     2.617 2.496
  ... (remaining 14131 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'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             2.470
  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:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     3.350
  Find NCS groups from input model:        0.010
  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:6.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
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      :  0.009   0.048   1758  Z= 0.420
  Angle     :  0.858   5.672   2352  Z= 0.475
  Chirality :  0.061   0.136    270
  Planarity :  0.003   0.012    288
  Dihedral  : 12.141  44.587    666
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 are not related in a simple way.
  whole: -3.48 (0.45), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.34), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.012   0.004   PHE C 100 
 TRP   0.002   0.001   TRP F  76 
 HIS   0.003   0.002   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00923 ( 1752)
  covalent geometry    : angle       0.85855 ( 2340)
  SS BOND              : bond        0.00618 (    6)
  SS BOND              : angle       0.62149 (   12)
  hydrogen bonds       : bond        0.16726 (   22)
  hydrogen bonds       : angle       7.50525 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.078 
Fit side-chains
REVERT: C   78 LYS cc_start: 0.8560 (mttt) cc_final: 0.8329 (mttm)
REVERT: C  104 LYS cc_start: 0.8015 (tttt) cc_final: 0.7802 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.9089
  time to fit residues: 37.6766
Evaluate side-chains
  34 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0370
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   chunk 4 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
A  90 ASN
B  75 ASN
B  90 ASN
D  75 ASN
D  90 ASN
F  75 ASN
F  90 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.155345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.133133 restraints weight = 1594.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 1.21
r_work: 0.3874 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3764 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   1758  Z= 0.106
  Angle     :  0.647   4.194   2352  Z= 0.336
  Chirality :  0.053   0.128    270
  Planarity :  0.002   0.010    288
  Dihedral  :  6.057  24.808    222
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.22 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.46), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.35), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 PHE   0.005   0.002   PHE E 100 
 TRP   0.001   0.000   TRP C  76 
 HIS   0.003   0.002   HIS F  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 1752)
  covalent geometry    : angle       0.64804 ( 2340)
  SS BOND              : bond        0.00226 (    6)
  SS BOND              : angle       0.51475 (   12)
  hydrogen bonds       : bond        0.01936 (   22)
  hydrogen bonds       : angle       6.59670 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8542 (mtpm) cc_final: 0.8222 (mtmt)
  outliers start: 4
  outliers final: 1
  residues processed: 43
  average time/residue: 0.8084
  time to fit residues: 35.1881
Evaluate side-chains
  40 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   97 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 3 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
C  90 ASN
E  90 ASN
D  75 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.154782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.132617 restraints weight = 1600.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 1.23
r_work: 0.3833 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3729 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   1758  Z= 0.180
  Angle     :  0.654   5.071   2352  Z= 0.351
  Chirality :  0.052   0.134    270
  Planarity :  0.003   0.016    288
  Dihedral  :  6.167  24.549    222
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.69 %
    Favored  : 81.37 %
  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 are not related in a simple way.
  whole: -3.01 (0.46), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.35), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 PHE   0.011   0.003   PHE E 100 
 TRP   0.002   0.001   TRP C  76 
 HIS   0.002   0.001   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 1752)
  covalent geometry    : angle       0.65395 ( 2340)
  SS BOND              : bond        0.00338 (    6)
  SS BOND              : angle       0.57667 (   12)
  hydrogen bonds       : bond        0.02331 (   22)
  hydrogen bonds       : angle       6.51886 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.048 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8616 (mtpm) cc_final: 0.8303 (mtmt)
REVERT: B   97 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7519 (t70)
REVERT: D   97 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7740 (t70)
  outliers start: 6
  outliers final: 3
  residues processed: 39
  average time/residue: 0.7628
  time to fit residues: 30.1165
Evaluate side-chains
  39 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain F residue   97 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0270
   chunk 5 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0870
   chunk 12 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.4416

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.165214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.142772 restraints weight = 1572.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.4036 rms_B_bonded: 1.17
r_work: 0.3955 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3858 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1758  Z= 0.088
  Angle     :  0.557   5.076   2352  Z= 0.295
  Chirality :  0.052   0.125    270
  Planarity :  0.002   0.008    288
  Dihedral  :  5.220  20.941    222
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.04 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.49), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.37), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  89 
 PHE   0.004   0.001   PHE E 100 
 TRP   0.002   0.001   TRP A  76 
 HIS   0.002   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 ( 1752)
  covalent geometry    : angle       0.55726 ( 2340)
  SS BOND              : bond        0.00242 (    6)
  SS BOND              : angle       0.46932 (   12)
  hydrogen bonds       : bond        0.01524 (   22)
  hydrogen bonds       : angle       6.22658 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8494 (mtpm) cc_final: 0.8226 (mtmt)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.6598
  time to fit residues: 29.4652
Evaluate side-chains
  37 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.155332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.133317 restraints weight = 1598.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 1.21
r_work: 0.3852 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3744 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   1758  Z= 0.198
  Angle     :  0.620   5.199   2352  Z= 0.339
  Chirality :  0.051   0.132    270
  Planarity :  0.002   0.010    288
  Dihedral  :  5.864  21.969    222
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.59 %
    Favored  : 75.98 %
  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 are not related in a simple way.
  whole: -2.84 (0.47), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 PHE   0.012   0.003   PHE E 100 
 TRP   0.003   0.001   TRP D  76 
 HIS   0.004   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 1752)
  covalent geometry    : angle       0.62030 ( 2340)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       0.56754 (   12)
  hydrogen bonds       : bond        0.02124 (   22)
  hydrogen bonds       : angle       6.45091 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.050 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8642 (mtpm) cc_final: 0.8365 (mtmt)
REVERT: B   97 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7568 (t70)
REVERT: E   89 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8068 (tmt90)
  outliers start: 7
  outliers final: 2
  residues processed: 37
  average time/residue: 0.7051
  time to fit residues: 26.3846
Evaluate side-chains
  37 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain E residue   89 ARG
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain F residue   97 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.152615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.130630 restraints weight = 1637.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 1.23
r_work: 0.3815 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
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      :  0.007   0.039   1758  Z= 0.299
  Angle     :  0.730   5.792   2352  Z= 0.402
  Chirality :  0.055   0.141    270
  Planarity :  0.003   0.014    288
  Dihedral  :  6.613  27.245    222
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.75 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.61 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.45), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.35), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 PHE   0.018   0.005   PHE E 100 
 TRP   0.005   0.001   TRP E  76 
 HIS   0.003   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 ( 1752)
  covalent geometry    : angle       0.73035 ( 2340)
  SS BOND              : bond        0.00504 (    6)
  SS BOND              : angle       0.71160 (   12)
  hydrogen bonds       : bond        0.02589 (   22)
  hydrogen bonds       : angle       6.59365 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.050 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8678 (mtpm) cc_final: 0.8395 (mtmt)
REVERT: A   97 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7531 (t70)
REVERT: C   75 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8194 (m110)
  outliers start: 7
  outliers final: 3
  residues processed: 37
  average time/residue: 0.5621
  time to fit residues: 21.0596
Evaluate side-chains
  37 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain F residue   97 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    1.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.157195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.135152 restraints weight = 1558.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 1.19
r_work: 0.3889 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3785 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1758  Z= 0.134
  Angle     :  0.608   6.213   2352  Z= 0.324
  Chirality :  0.052   0.134    270
  Planarity :  0.002   0.010    288
  Dihedral  :  5.918  24.011    222
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.06 %
    Favored  : 74.51 %
  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 are not related in a simple way.
  whole: -2.80 (0.47), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  89 
 PHE   0.008   0.002   PHE E 100 
 TRP   0.003   0.001   TRP D  76 
 HIS   0.003   0.002   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 1752)
  covalent geometry    : angle       0.60897 ( 2340)
  SS BOND              : bond        0.00276 (    6)
  SS BOND              : angle       0.45704 (   12)
  hydrogen bonds       : bond        0.01755 (   22)
  hydrogen bonds       : angle       6.49409 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.047 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8609 (mtpm) cc_final: 0.8322 (mtmt)
REVERT: D   97 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7673 (t70)
  outliers start: 7
  outliers final: 2
  residues processed: 37
  average time/residue: 0.5034
  time to fit residues: 18.8927
Evaluate side-chains
  36 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain F residue   97 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 17 optimal weight:    0.1980
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0980
   chunk 8 optimal weight:    0.0040
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.8594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.160096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.137838 restraints weight = 1558.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 1.18
r_work: 0.3904 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3803 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1758  Z= 0.112
  Angle     :  0.574   5.994   2352  Z= 0.305
  Chirality :  0.051   0.130    270
  Planarity :  0.002   0.009    288
  Dihedral  :  5.501  21.699    222
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 24.51 %
    Favored  : 74.51 %
  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 are not related in a simple way.
  whole: -2.60 (0.49), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.37), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  89 
 PHE   0.006   0.002   PHE E 100 
 TRP   0.003   0.001   TRP B  76 
 HIS   0.003   0.002   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 1752)
  covalent geometry    : angle       0.57436 ( 2340)
  SS BOND              : bond        0.00237 (    6)
  SS BOND              : angle       0.42244 (   12)
  hydrogen bonds       : bond        0.01723 (   22)
  hydrogen bonds       : angle       6.41534 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8556 (mtpm) cc_final: 0.8244 (mtmt)
  outliers start: 2
  outliers final: 1
  residues processed: 37
  average time/residue: 0.4833
  time to fit residues: 18.1540
Evaluate side-chains
  37 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   97 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.157693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.135874 restraints weight = 1617.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.4000 rms_B_bonded: 1.18
r_work: 0.3922 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3822 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1758  Z= 0.127
  Angle     :  0.579   6.106   2352  Z= 0.310
  Chirality :  0.051   0.131    270
  Planarity :  0.002   0.009    288
  Dihedral  :  5.525  21.476    222
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 24.51 %
    Favored  : 74.51 %
  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 are not related in a simple way.
  whole: -2.58 (0.49), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.38), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  89 
 PHE   0.007   0.002   PHE E 100 
 TRP   0.003   0.001   TRP B  76 
 HIS   0.003   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 1752)
  covalent geometry    : angle       0.58010 ( 2340)
  SS BOND              : bond        0.00253 (    6)
  SS BOND              : angle       0.44691 (   12)
  hydrogen bonds       : bond        0.01754 (   22)
  hydrogen bonds       : angle       6.45442 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.052 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8578 (mtpm) cc_final: 0.8264 (mtmt)
  outliers start: 2
  outliers final: 2
  residues processed: 36
  average time/residue: 0.5212
  time to fit residues: 19.0382
Evaluate side-chains
  38 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain F residue   97 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0770
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 0 optimal weight:    0.7980
   overall best weight:    0.9740

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.159605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.137461 restraints weight = 1563.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 1.19
r_work: 0.3911 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3803 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1758  Z= 0.119
  Angle     :  0.576   6.376   2352  Z= 0.307
  Chirality :  0.051   0.130    270
  Planarity :  0.002   0.009    288
  Dihedral  :  5.484  21.197    222
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 24.51 %
    Favored  : 74.51 %
  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 are not related in a simple way.
  whole: -2.56 (0.50), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.38), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  89 
 PHE   0.007   0.002   PHE E 100 
 TRP   0.003   0.001   TRP B  76 
 HIS   0.003   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 1752)
  covalent geometry    : angle       0.57679 ( 2340)
  SS BOND              : bond        0.00232 (    6)
  SS BOND              : angle       0.44678 (   12)
  hydrogen bonds       : bond        0.01729 (   22)
  hydrogen bonds       : angle       6.42858 (   66)

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

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

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  408 Ramachandran restraints generated.
    204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.045 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8586 (mtpm) cc_final: 0.8275 (mtmt)
  outliers start: 2
  outliers final: 2
  residues processed: 36
  average time/residue: 0.4646
  time to fit residues: 16.9567
Evaluate side-chains
  38 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain F residue   97 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 12 optimal weight:    0.4980
   chunk 5 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.0182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.158685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.136435 restraints weight = 1600.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 1.21
r_work: 0.3901 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3799 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   1758  Z= 0.122
  Angle     :  0.572   6.081   2352  Z= 0.306
  Chirality :  0.051   0.129    270
  Planarity :  0.002   0.009    288
  Dihedral  :  5.456  20.851    222
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.53 %
    Favored  : 74.51 %
  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 are not related in a simple way.
  whole: -2.55 (0.50), residues: 204
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.38), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  89 
 PHE   0.007   0.002   PHE E 100 
 TRP   0.003   0.001   TRP B  76 
 HIS   0.003   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 1752)
  covalent geometry    : angle       0.57274 ( 2340)
  SS BOND              : bond        0.00242 (    6)
  SS BOND              : angle       0.43893 (   12)
  hydrogen bonds       : bond        0.01736 (   22)
  hydrogen bonds       : angle       6.44316 (   66)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1090.83 seconds
wall clock time: 19 minutes 7.75 seconds (1147.75 seconds total)