Starting phenix.real_space_refine
on Tue Feb  3 12:20:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j4e_61133/02_2026/9j4e_61133.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j4e_61133/02_2026/9j4e_61133.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j4e_61133/02_2026/9j4e_61133.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j4e_61133/02_2026/9j4e_61133.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j4e_61133/02_2026/9j4e_61133.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j4e_61133/02_2026/9j4e_61133.cif"
  }
  resolution = 3.32
  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=   0.003
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    1092      2.51       5
     N     324      2.21       5
     O     324      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 1758
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "E"
      Number of atoms: 293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 293
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
  Restraints were copied for chains:
    F, A, C, B, D
  Time building chain proxies: 0.40, per 1000 atoms: 0.23
  Number of scatterers: 1758
  At special positions: 0
  Unit cell: (83.74, 85.86, 30.74, 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     324      8.00
     N     324      7.00
     C    1092      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  80 " - pdb=" SG  CYS E  83 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F  80 " - pdb=" SG  CYS F  83 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  80 " - pdb=" SG  CYS A  83 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  80 " - pdb=" SG  CYS C  83 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  80 " - pdb=" SG  CYS B  83 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  80 " - pdb=" SG  CYS D  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: 0.16
  Conformation dependent library (CDL) restraints added in 79.8 milliseconds
  

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 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 6 sheets defined
      0.0% alpha, 29.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73
      removed outlier: 6.587A  pdb=" N   MET E  71 " --> pdb=" O   HIS B  72 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81
      removed outlier: 6.630A  pdb=" N   CYS E  80 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 96
      removed outlier: 6.160A  pdb=" N   ASN E  90 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   VAL A  93 " --> pdb=" O   ASN E  90 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR E  92 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   ASP A  95 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   THR E  94 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL B  96 " --> pdb=" O   ASP E  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 70 through 73
      removed outlier: 6.593A  pdb=" N   MET F  71 " --> pdb=" O   HIS D  72 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 81
      removed outlier: 6.630A  pdb=" N   CYS F  80 " --> pdb=" O   LYS C  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 96
      removed outlier: 6.160A  pdb=" N   ASN F  90 " --> pdb=" O   VAL C  91 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   VAL C  93 " --> pdb=" O   ASN F  90 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR F  92 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   ASP C  95 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
      removed outlier: 8.668A  pdb=" N   THR F  94 " --> pdb=" O   ASP C  95 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   VAL D  96 " --> pdb=" O   ASP F  95 " (cutoff:3.500A)

    20 hydrogen bonds defined for protein.
    60 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: 0.20

  Time building geometry restraints manager: 0.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 576
        1.34 -     1.45: 191
        1.45 -     1.57: 985
        1.57 -     1.68: 0
        1.68 -     1.80: 24
  Bond restraints: 1776
  Sorted by residual:
  bond pdb=" CA  THR E  94 "
       pdb=" CB  THR E  94 "
    ideal  model  delta    sigma   weight residual
    1.533  1.508  0.026 1.72e-02 3.38e+03 2.26e+00
  bond pdb=" CA  THR B  94 "
       pdb=" CB  THR B  94 "
    ideal  model  delta    sigma   weight residual
    1.533  1.508  0.026 1.72e-02 3.38e+03 2.22e+00
  bond pdb=" CA  THR F  94 "
       pdb=" CB  THR F  94 "
    ideal  model  delta    sigma   weight residual
    1.533  1.508  0.025 1.72e-02 3.38e+03 2.18e+00
  bond pdb=" CA  THR C  94 "
       pdb=" CB  THR C  94 "
    ideal  model  delta    sigma   weight residual
    1.533  1.508  0.025 1.72e-02 3.38e+03 2.17e+00
  bond pdb=" CA  THR D  94 "
       pdb=" CB  THR D  94 "
    ideal  model  delta    sigma   weight residual
    1.533  1.509  0.025 1.72e-02 3.38e+03 2.09e+00
  ... (remaining 1771 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 2050
        1.31 -     2.63: 271
        2.63 -     3.94: 37
        3.94 -     5.26: 6
        5.26 -     6.57: 6
  Bond angle restraints: 2370
  Sorted by residual:
  angle pdb=" N   TRP E  76 "
        pdb=" CA  TRP E  76 "
        pdb=" C   TRP E  76 "
      ideal   model   delta    sigma   weight residual
     111.28  114.66   -3.38 1.35e+00 5.49e-01 6.28e+00
  angle pdb=" N   TRP B  76 "
        pdb=" CA  TRP B  76 "
        pdb=" C   TRP B  76 "
      ideal   model   delta    sigma   weight residual
     111.28  114.63   -3.35 1.35e+00 5.49e-01 6.16e+00
  angle pdb=" N   TRP C  76 "
        pdb=" CA  TRP C  76 "
        pdb=" C   TRP C  76 "
      ideal   model   delta    sigma   weight residual
     111.28  114.63   -3.35 1.35e+00 5.49e-01 6.16e+00
  angle pdb=" N   TRP A  76 "
        pdb=" CA  TRP A  76 "
        pdb=" C   TRP A  76 "
      ideal   model   delta    sigma   weight residual
     111.28  114.62   -3.34 1.35e+00 5.49e-01 6.13e+00
  angle pdb=" N   TRP D  76 "
        pdb=" CA  TRP D  76 "
        pdb=" C   TRP D  76 "
      ideal   model   delta    sigma   weight residual
     111.28  114.62   -3.34 1.35e+00 5.49e-01 6.13e+00
  ... (remaining 2365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    14.14: 954
       14.14 -    28.28: 90
       28.28 -    42.42: 36
       42.42 -    56.56: 12
       56.56 -    70.70: 6
  Dihedral angle restraints: 1098
    sinusoidal: 474
      harmonic: 624
  Sorted by residual:
  dihedral pdb=" CB  CYS E  80 "
           pdb=" SG  CYS E  80 "
           pdb=" SG  CYS E  83 "
           pdb=" CB  CYS E  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   22.30   70.70     1      1.00e+01 1.00e-02 6.43e+01
  dihedral pdb=" CB  CYS D  80 "
           pdb=" SG  CYS D  80 "
           pdb=" SG  CYS D  83 "
           pdb=" CB  CYS D  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   22.31   70.69     1      1.00e+01 1.00e-02 6.43e+01
  dihedral pdb=" CB  CYS B  80 "
           pdb=" SG  CYS B  80 "
           pdb=" SG  CYS B  83 "
           pdb=" CB  CYS B  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   22.35   70.65     1      1.00e+01 1.00e-02 6.42e+01
  ... (remaining 1095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 116
       0.036 -    0.071: 79
       0.071 -    0.106: 44
       0.106 -    0.142: 25
       0.142 -    0.177: 6
  Chirality restraints: 270
  Sorted by residual:
  chirality pdb=" CA  TRP E  76 "
            pdb=" N   TRP E  76 "
            pdb=" C   TRP E  76 "
            pdb=" CB  TRP E  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  TRP C  76 "
            pdb=" N   TRP C  76 "
            pdb=" C   TRP C  76 "
            pdb=" CB  TRP C  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.76e-01
  chirality pdb=" CA  TRP F  76 "
            pdb=" N   TRP F  76 "
            pdb=" C   TRP F  76 "
            pdb=" CB  TRP F  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.75e-01
  ... (remaining 267 not shown)

  Planarity restraints: 294
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP D  76 "    0.005 2.00e-02 2.50e+03   1.06e-02 1.12e+00
        pdb=" C   TRP D  76 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   TRP D  76 "    0.007 2.00e-02 2.50e+03
        pdb=" N   SER D  77 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP F  76 "    0.005 2.00e-02 2.50e+03   1.04e-02 1.09e+00
        pdb=" C   TRP F  76 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   TRP F  76 "    0.007 2.00e-02 2.50e+03
        pdb=" N   SER F  77 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP E  76 "   -0.005 2.00e-02 2.50e+03   1.04e-02 1.09e+00
        pdb=" C   TRP E  76 "    0.018 2.00e-02 2.50e+03
        pdb=" O   TRP E  76 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   SER E  77 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 291 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 670
        2.85 -     3.36: 1421
        3.36 -     3.88: 2594
        3.88 -     4.39: 2751
        4.39 -     4.90: 5713
  Nonbonded interactions: 13149
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS E 102 "
            pdb=" OD1 ASP B  82 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" NZ  LYS F 102 "
            pdb=" OD1 ASP D  82 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" OD1 ASP E  82 "
            pdb=" NZ  LYS A 102 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OD1 ASP F  82 "
            pdb=" NZ  LYS C 102 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" N   TRP E  76 "
            pdb=" O   TRP B  76 "
     model   vdw
     2.368 3.120
  ... (remaining 13144 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 'E'
  selection = chain 'F'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

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:             1.520
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.400
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
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      :  0.010   0.044   1782  Z= 0.450
  Angle     :  0.957   6.573   2382  Z= 0.556
  Chirality :  0.065   0.177    270
  Planarity :  0.004   0.011    294
  Dihedral  : 13.001  44.356    672
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 18.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.14 %
    Favored  : 82.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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: -4.90 (0.38), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.29), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  69 
 PHE   0.011   0.005   PHE B 100 
 TRP   0.007   0.002   TRP B  76 
 HIS   0.001   0.000   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00986 ( 1776)
  covalent geometry    : angle       0.95592 ( 2370)
  SS BOND              : bond        0.00900 (    6)
  SS BOND              : angle       1.07348 (   12)
  hydrogen bonds       : bond        0.30879 (   20)
  hydrogen bonds       : angle       9.84586 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.045 
Fit side-chains
REVERT: A   71 MET cc_start: 0.7153 (mtt) cc_final: 0.6902 (mtp)
REVERT: A  104 LYS cc_start: 0.8196 (mttt) cc_final: 0.7899 (mttp)
REVERT: C   71 MET cc_start: 0.7200 (mtt) cc_final: 0.6401 (mtp)
REVERT: B   71 MET cc_start: 0.8067 (mtt) cc_final: 0.7781 (mtp)
REVERT: D   71 MET cc_start: 0.7546 (mtt) cc_final: 0.7185 (mtp)
REVERT: D   74 LYS cc_start: 0.7853 (mttp) cc_final: 0.7605 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1406
  time to fit residues: 3.6247
Evaluate side-chains
  15 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.045 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.8982

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.155192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.134609 restraints weight = 2661.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.4318 rms_B_bonded: 3.31
r_work: 0.4212 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1782  Z= 0.110
  Angle     :  0.599   4.849   2382  Z= 0.330
  Chirality :  0.052   0.138    270
  Planarity :  0.002   0.010    294
  Dihedral  :  4.915  13.155    228
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.43 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  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: -4.23 (0.44), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.22 (0.33), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  89 
 PHE   0.005   0.002   PHE C 100 
 TRP   0.006   0.001   TRP B  76 
 HIS   0.003   0.002   HIS F  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 1776)
  covalent geometry    : angle       0.59833 ( 2370)
  SS BOND              : bond        0.00060 (    6)
  SS BOND              : angle       0.75241 (   12)
  hydrogen bonds       : bond        0.03409 (   20)
  hydrogen bonds       : angle       6.55546 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A   71 MET cc_start: 0.6717 (mtt) cc_final: 0.6502 (mtp)
REVERT: C   71 MET cc_start: 0.7072 (mtt) cc_final: 0.6243 (mtp)
REVERT: B   71 MET cc_start: 0.7939 (mtt) cc_final: 0.7605 (mtp)
REVERT: D   71 MET cc_start: 0.7525 (mtt) cc_final: 0.7109 (mtp)
REVERT: D   74 LYS cc_start: 0.7782 (mttp) cc_final: 0.7441 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1257
  time to fit residues: 2.7886
Evaluate side-chains
  12 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.4654 r_free = 0.4654 target = 0.164500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.146614 restraints weight = 2714.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.4419 rms_B_bonded: 2.62
r_work: 0.4327 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.4219 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   1782  Z= 0.162
  Angle     :  0.700  10.379   2382  Z= 0.358
  Chirality :  0.056   0.246    270
  Planarity :  0.002   0.010    294
  Dihedral  :  4.746  13.032    228
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.37 %
    Favored  : 93.14 %
  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: -4.22 (0.43), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.33), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  89 
 PHE   0.005   0.002   PHE D 100 
 TRP   0.005   0.001   TRP D  76 
 HIS   0.003   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 1776)
  covalent geometry    : angle       0.69965 ( 2370)
  SS BOND              : bond        0.00239 (    6)
  SS BOND              : angle       0.84589 (   12)
  hydrogen bonds       : bond        0.03039 (   20)
  hydrogen bonds       : angle       5.83945 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 11
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A   71 MET cc_start: 0.6941 (mtt) cc_final: 0.6710 (mtp)
REVERT: C   71 MET cc_start: 0.6956 (mtt) cc_final: 0.6309 (mtp)
REVERT: B   71 MET cc_start: 0.7900 (mtt) cc_final: 0.7586 (mtp)
REVERT: B   74 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7527 (mmtm)
REVERT: D   74 LYS cc_start: 0.7791 (mttp) cc_final: 0.7416 (mmtm)
  outliers start: 1
  outliers final: 1
  residues processed: 12
  average time/residue: 0.1289
  time to fit residues: 1.7576
Evaluate side-chains
  12 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 11
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   85 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 6 optimal weight:    0.0020
   chunk 7 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   chunk 12 optimal weight:    0.0060
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6004

-------------------------------------------------------------------------------
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 = 0.4625 r_free = 0.4625 target = 0.159351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.138896 restraints weight = 2606.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.4357 rms_B_bonded: 3.13
r_work: 0.4260 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   1782  Z= 0.081
  Angle     :  0.551   7.372   2382  Z= 0.294
  Chirality :  0.052   0.204    270
  Planarity :  0.002   0.009    294
  Dihedral  :  4.140  11.014    228
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  7.35 %
    Favored  : 92.16 %
  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: -3.92 (0.44), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.34), residues: 210

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00167 ( 1776)
  covalent geometry    : angle       0.55088 ( 2370)
  SS BOND              : bond        0.00079 (    6)
  SS BOND              : angle       0.60401 (   12)
  hydrogen bonds       : bond        0.02042 (   20)
  hydrogen bonds       : angle       5.75619 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.076 
Fit side-chains
REVERT: E   71 MET cc_start: 0.7507 (mtt) cc_final: 0.7252 (mtp)
REVERT: A   71 MET cc_start: 0.6718 (mtt) cc_final: 0.6365 (mtp)
REVERT: C   71 MET cc_start: 0.6820 (mtt) cc_final: 0.6151 (mtp)
REVERT: B   71 MET cc_start: 0.7889 (mtt) cc_final: 0.7632 (mtp)
REVERT: D   74 LYS cc_start: 0.7628 (mttp) cc_final: 0.7376 (mmtm)
  outliers start: 1
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0898
  time to fit residues: 1.5753
Evaluate side-chains
  10 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0770
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.8146

-------------------------------------------------------------------------------
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 = 0.4542 r_free = 0.4542 target = 0.151929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.132495 restraints weight = 2684.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.4283 rms_B_bonded: 3.23
r_work: 0.4181 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   1782  Z= 0.143
  Angle     :  0.641  10.566   2382  Z= 0.331
  Chirality :  0.052   0.239    270
  Planarity :  0.002   0.008    294
  Dihedral  :  4.312  11.147    228
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.76 %
    Favored  : 85.24 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  6.86 %
    Favored  : 91.67 %
  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: -3.94 (0.45), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.35), residues: 210

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 1776)
  covalent geometry    : angle       0.64037 ( 2370)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       0.76860 (   12)
  hydrogen bonds       : bond        0.02395 (   20)
  hydrogen bonds       : angle       5.34727 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.6776 (mtt) cc_final: 0.6248 (mtp)
REVERT: C   71 MET cc_start: 0.6941 (mtt) cc_final: 0.6305 (mtp)
REVERT: B   71 MET cc_start: 0.7811 (mtt) cc_final: 0.7359 (mtp)
REVERT: D   71 MET cc_start: 0.7561 (mtt) cc_final: 0.7035 (mtp)
  outliers start: 3
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0943
  time to fit residues: 1.5432
Evaluate side-chains
  13 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain F residue   85 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 6 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 9 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    2.5384

-------------------------------------------------------------------------------
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 = 0.4606 r_free = 0.4606 target = 0.159009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.140592 restraints weight = 2635.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.4257 rms_B_bonded: 2.84
r_work: 0.4159 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.4036 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   1782  Z= 0.189
  Angle     :  0.681  10.090   2382  Z= 0.354
  Chirality :  0.052   0.237    270
  Planarity :  0.002   0.009    294
  Dihedral  :  4.593  10.821    228
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.19 %
    Favored  : 83.81 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  6.37 %
    Favored  : 90.69 %
  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: -4.02 (0.45), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.34), residues: 210

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 1776)
  covalent geometry    : angle       0.68002 ( 2370)
  SS BOND              : bond        0.00266 (    6)
  SS BOND              : angle       0.85933 (   12)
  hydrogen bonds       : bond        0.02605 (   20)
  hydrogen bonds       : angle       5.31367 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 11
  time to evaluate  : 0.049 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.6853 (mtt) cc_final: 0.6145 (mtp)
REVERT: C   71 MET cc_start: 0.6836 (mtt) cc_final: 0.6107 (mtp)
REVERT: B   71 MET cc_start: 0.7768 (mtt) cc_final: 0.7505 (mtp)
REVERT: D   71 MET cc_start: 0.7561 (mtt) cc_final: 0.6973 (mtp)
  outliers start: 6
  outliers final: 5
  residues processed: 17
  average time/residue: 0.0666
  time to fit residues: 1.3266
Evaluate side-chains
  16 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   85 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 11 optimal weight:    0.0030
   chunk 10 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0040
   overall best weight:    0.4402

-------------------------------------------------------------------------------
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 = 0.4754 r_free = 0.4754 target = 0.169063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.150073 restraints weight = 2415.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.4404 rms_B_bonded: 2.92
r_work: 0.4305 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   1782  Z= 0.076
  Angle     :  0.552   8.110   2382  Z= 0.288
  Chirality :  0.053   0.226    270
  Planarity :  0.002   0.009    294
  Dihedral  :  3.865  11.162    228
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  8.82 %
    Favored  : 90.69 %
  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: -3.78 (0.46), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.35), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  69 
 PHE   0.004   0.001   PHE C 100 
 TRP   0.004   0.000   TRP A  76 
 HIS   0.003   0.001   HIS E  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00155 ( 1776)
  covalent geometry    : angle       0.55125 ( 2370)
  SS BOND              : bond        0.00110 (    6)
  SS BOND              : angle       0.60518 (   12)
  hydrogen bonds       : bond        0.01815 (   20)
  hydrogen bonds       : angle       5.76173 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 9
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A   71 MET cc_start: 0.6584 (mtt) cc_final: 0.6221 (mtp)
REVERT: C   71 MET cc_start: 0.6779 (mtt) cc_final: 0.6270 (mtp)
REVERT: B   71 MET cc_start: 0.7593 (mtt) cc_final: 0.7305 (mtt)
REVERT: D   71 MET cc_start: 0.7545 (mtt) cc_final: 0.7008 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 10
  average time/residue: 0.0772
  time to fit residues: 0.9740
Evaluate side-chains
  9 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 8
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   85 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.4547 r_free = 0.4547 target = 0.152144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.132780 restraints weight = 2725.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.4284 rms_B_bonded: 3.20
r_work: 0.4177 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1782  Z= 0.140
  Angle     :  0.620  11.100   2382  Z= 0.323
  Chirality :  0.050   0.225    270
  Planarity :  0.002   0.010    294
  Dihedral  :  4.197  12.907    228
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.24 %
    Favored  : 84.76 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  7.84 %
    Favored  : 90.20 %
  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: -3.85 (0.47), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.35), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.005   0.002   PHE D 100 
 TRP   0.004   0.001   TRP B  76 
 HIS   0.002   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 1776)
  covalent geometry    : angle       0.61955 ( 2370)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       0.74284 (   12)
  hydrogen bonds       : bond        0.02127 (   20)
  hydrogen bonds       : angle       5.37194 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.046 
Fit side-chains
REVERT: A   71 MET cc_start: 0.6796 (mtt) cc_final: 0.6352 (mtp)
REVERT: C   71 MET cc_start: 0.6811 (mtt) cc_final: 0.6215 (mtp)
REVERT: D   71 MET cc_start: 0.7497 (mtt) cc_final: 0.6914 (mtp)
  outliers start: 4
  outliers final: 4
  residues processed: 15
  average time/residue: 0.0826
  time to fit residues: 1.4354
Evaluate side-chains
  15 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain C residue   77 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0470
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.7884

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.152607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.133332 restraints weight = 2733.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.4281 rms_B_bonded: 3.18
r_work: 0.4176 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1782  Z= 0.140
  Angle     :  0.627  10.726   2382  Z= 0.325
  Chirality :  0.050   0.220    270
  Planarity :  0.002   0.010    294
  Dihedral  :  4.278  12.688    228
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.71 %
    Favored  : 84.29 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  7.35 %
    Favored  : 90.20 %
  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: -3.84 (0.46), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.35), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.005   0.002   PHE D 100 
 TRP   0.005   0.001   TRP D  76 
 HIS   0.002   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 1776)
  covalent geometry    : angle       0.62595 ( 2370)
  SS BOND              : bond        0.00205 (    6)
  SS BOND              : angle       0.73935 (   12)
  hydrogen bonds       : bond        0.02201 (   20)
  hydrogen bonds       : angle       5.37104 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 10
  time to evaluate  : 0.044 
Fit side-chains
REVERT: A   71 MET cc_start: 0.6676 (mtt) cc_final: 0.6291 (mtp)
REVERT: C   71 MET cc_start: 0.6776 (mtt) cc_final: 0.6148 (mtp)
  outliers start: 5
  outliers final: 5
  residues processed: 15
  average time/residue: 0.0429
  time to fit residues: 0.8284
Evaluate side-chains
  15 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 10
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    0.1980
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.4583 r_free = 0.4583 target = 0.154146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.134437 restraints weight = 2643.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.4310 rms_B_bonded: 3.16
r_work: 0.4209 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   1782  Z= 0.117
  Angle     :  0.631  10.513   2382  Z= 0.323
  Chirality :  0.050   0.229    270
  Planarity :  0.002   0.010    294
  Dihedral  :  4.430  14.838    228
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  9.80 %
    Favored  : 88.24 %
  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: -3.86 (0.46), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.35), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  69 
 PHE   0.004   0.001   PHE D 100 
 TRP   0.007   0.001   TRP E  76 
 HIS   0.002   0.001   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 1776)
  covalent geometry    : angle       0.63070 ( 2370)
  SS BOND              : bond        0.00136 (    6)
  SS BOND              : angle       0.70728 (   12)
  hydrogen bonds       : bond        0.02296 (   20)
  hydrogen bonds       : angle       5.72496 (   60)

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

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

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  420 Ramachandran restraints generated.
    210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 9
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A   71 MET cc_start: 0.6570 (mtt) cc_final: 0.6319 (mtp)
REVERT: C   71 MET cc_start: 0.6838 (mtt) cc_final: 0.6201 (mtp)
  outliers start: 4
  outliers final: 4
  residues processed: 13
  average time/residue: 0.0464
  time to fit residues: 0.7770
Evaluate side-chains
  13 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 9
  time to evaluate  : 0.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 5 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 7 optimal weight:    0.6980
   chunk 13 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 3 optimal weight:   20.0000
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.5007 r_free = 0.5007 target = 0.190895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.171772 restraints weight = 2197.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.4372 rms_B_bonded: 2.43
r_work: 0.4278 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4175 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   1782  Z= 0.104
  Angle     :  0.593   9.901   2382  Z= 0.308
  Chirality :  0.050   0.219    270
  Planarity :  0.002   0.010    294
  Dihedral  :  4.264  14.924    228
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.81 %
    Favored  : 86.19 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  9.31 %
    Favored  : 88.73 %
  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 are not related in a simple way.
  whole: -3.76 (0.46), residues: 210
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.86 (0.35), residues: 210

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 1776)
  covalent geometry    : angle       0.59248 ( 2370)
  SS BOND              : bond        0.00154 (    6)
  SS BOND              : angle       0.69758 (   12)
  hydrogen bonds       : bond        0.02171 (   20)
  hydrogen bonds       : angle       5.81656 (   60)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 667.49 seconds
wall clock time: 12 minutes 5.58 seconds (725.58 seconds total)