Starting phenix.real_space_refine
on Fri Aug 22 12:38:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlw_36406/08_2025/8jlw_36406.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlw_36406/08_2025/8jlw_36406.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlw_36406/08_2025/8jlw_36406.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlw_36406/08_2025/8jlw_36406.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlw_36406/08_2025/8jlw_36406.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlw_36406/08_2025/8jlw_36406.cif"
  }
  resolution = 3.0
  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=   0.037
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      19      5.16       5
     C    1352      2.51       5
     N     364      2.21       5
     O     422      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2157
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 424
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 911
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 822
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
  Time building chain proxies: 0.54, per 1000 atoms: 0.25
  Number of scatterers: 2157
  At special positions: 0
  Unit cell: (55.1, 66.5, 77.9, 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      19     16.00
     O     422      8.00
     N     364      7.00
     C    1352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1165 " - pdb=" SG  CYS A1198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1169 " - pdb=" SG  CYS A1205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1173 " - pdb=" SG  CYS A1207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1193 " - pdb=" SG  CYS A1360 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1208 " - pdb=" SG  CYS A1368 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.10
  Conformation dependent library (CDL) restraints added in 52.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  500

  Finding SS restraints...
    Secondary structure from input PDB file:
      1 helices and 7 sheets defined
      1.8% alpha, 38.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.562A  pdb=" N   SER H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1162 through 1164
      removed outlier: 3.595A  pdb=" N   CYS A1205 " --> pdb=" O   THR A1164 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 12
      removed outlier: 3.751A  pdb=" N   SER H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   MET H  34 " --> pdb=" O   ALA H  50 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ALA H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   THR H  40 " --> pdb=" O   GLY H  44 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLY H  44 " --> pdb=" O   THR H  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 9 through 12
      removed outlier: 4.043A  pdb=" N   PHE H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 21
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.626A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU L  33 " --> pdb=" O   SER L  49 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   SER L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    72 hydrogen bonds defined for protein.
    165 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: 0.18

  Time building geometry restraints manager: 0.15 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: 679
        1.34 -     1.46: 607
        1.46 -     1.58: 906
        1.58 -     1.70: 0
        1.70 -     1.82: 24
  Bond restraints: 2216
  Sorted by residual:
  bond pdb=" C   SER L   7 "
       pdb=" N   PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 8.70e-03 1.32e+04 3.22e+00
  bond pdb=" CB  CYS H  96 "
       pdb=" SG  CYS H  96 "
    ideal  model  delta    sigma   weight residual
    1.808  1.765  0.043 3.30e-02 9.18e+02 1.71e+00
  bond pdb=" CB  VAL A1201 "
       pdb=" CG2 VAL A1201 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.14e+00
  bond pdb=" CB  LYS H  63 "
       pdb=" CG  LYS H  63 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.43e-01
  bond pdb=" CA  SER L  49 "
       pdb=" CB  SER L  49 "
    ideal  model  delta    sigma   weight residual
    1.536  1.516  0.020 2.08e-02 2.31e+03 9.11e-01
  ... (remaining 2211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 2860
        1.46 -     2.93: 121
        2.93 -     4.39: 18
        4.39 -     5.85: 2
        5.85 -     7.31: 2
  Bond angle restraints: 3003
  Sorted by residual:
  angle pdb=" C   CYS A1193 "
        pdb=" N   ASN A1194 "
        pdb=" CA  ASN A1194 "
      ideal   model   delta    sigma   weight residual
     120.97  128.24   -7.27 2.84e+00 1.24e-01 6.56e+00
  angle pdb=" CB  LYS H  63 "
        pdb=" CG  LYS H  63 "
        pdb=" CD  LYS H  63 "
      ideal   model   delta    sigma   weight residual
     111.30  116.69   -5.39 2.30e+00 1.89e-01 5.50e+00
  angle pdb=" C   GLN H 101 "
        pdb=" N   TYR H 102 "
        pdb=" CA  TYR H 102 "
      ideal   model   delta    sigma   weight residual
     121.54  125.85   -4.31 1.91e+00 2.74e-01 5.09e+00
  angle pdb=" CA  ILE L  94 "
        pdb=" C   ILE L  94 "
        pdb=" N   PRO L  95 "
      ideal   model   delta    sigma   weight residual
     118.88  122.25   -3.37 1.54e+00 4.22e-01 4.78e+00
  angle pdb=" C   HIS L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  125.66   -4.12 1.91e+00 2.74e-01 4.65e+00
  ... (remaining 2998 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 1136
       15.98 -    31.95: 121
       31.95 -    47.92: 30
       47.92 -    63.90: 11
       63.90 -    79.87: 2
  Dihedral angle restraints: 1300
    sinusoidal: 508
      harmonic: 792
  Sorted by residual:
  dihedral pdb=" CB  CYS A1169 "
           pdb=" SG  CYS A1169 "
           pdb=" SG  CYS A1205 "
           pdb=" CB  CYS A1205 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.75   61.25     1      1.00e+01 1.00e-02 4.98e+01
  dihedral pdb=" CA  ASN L  28 "
           pdb=" C   ASN L  28 "
           pdb=" N   ILE L  29 "
           pdb=" CA  ILE L  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.52   21.48     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.66   33.34     1      1.00e+01 1.00e-02 1.58e+01
  ... (remaining 1297 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 219
       0.041 -    0.083: 68
       0.083 -    0.124: 20
       0.124 -    0.165: 1
       0.165 -    0.206: 1
  Chirality restraints: 309
  Sorted by residual:
  chirality pdb=" CB  ILE L  94 "
            pdb=" CA  ILE L  94 "
            pdb=" CG1 ILE L  94 "
            pdb=" CG2 ILE L  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ILE L  75 "
            pdb=" N   ILE L  75 "
            pdb=" C   ILE L  75 "
            pdb=" CB  ILE L  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  VAL H  37 "
            pdb=" N   VAL H  37 "
            pdb=" C   VAL H  37 "
            pdb=" CB  VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.43e-01
  ... (remaining 306 not shown)

  Planarity restraints: 384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   7 "    0.048 5.00e-02 4.00e+02   7.31e-02 8.55e+00
        pdb=" N   PRO L   8 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1194 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.83e+00
        pdb=" N   PRO A1195 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A1195 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1195 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H  13 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.54e+00
        pdb=" N   PRO H  14 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "    0.022 5.00e-02 4.00e+02
  ... (remaining 381 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 499
        2.78 -     3.31: 1850
        3.31 -     3.84: 3402
        3.84 -     4.37: 4093
        4.37 -     4.90: 7323
  Nonbonded interactions: 17167
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP H  73 "
            pdb=" OG  SER H  75 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   PRO H   7 "
            pdb=" OG1 THR H 113 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" ND2 ASN A1194 "
            pdb=" O   CYS A1198 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" ND2 ASN H  55 "
            pdb=" OD2 ASP H  57 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" O   TRP H  47 "
            pdb=" ND2 ASN H  61 "
     model   vdw
     2.335 3.120
  ... (remaining 17162 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.850
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     2.630
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:4.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
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      :  0.005   0.043   2223  Z= 0.199
  Angle     :  0.702   7.315   3017  Z= 0.376
  Chirality :  0.043   0.206    309
  Planarity :  0.006   0.073    384
  Dihedral  : 14.614  79.870    779
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.65 (0.50), residues: 122
  loop : -1.55 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  61 
 TYR   0.014   0.003   TYR A1359 
 PHE   0.008   0.001   PHE L  98 
 TRP   0.011   0.002   TRP A1197 
 HIS   0.006   0.002   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 2216)
  covalent geometry    : angle       0.69427 ( 3003)
  SS BOND              : bond        0.00533 (    7)
  SS BOND              : angle       1.66062 (   14)
  hydrogen bonds       : bond        0.14662 (   65)
  hydrogen bonds       : angle       8.30483 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.048 
Fit side-chains
REVERT: H   39 GLN cc_start: 0.7078 (pt0) cc_final: 0.6315 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.4816
  time to fit residues: 21.1487
Evaluate side-chains
  34 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 1 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 = 0.4352 r_free = 0.4352 target = 0.210441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.190362 restraints weight = 2493.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.4166 rms_B_bonded: 2.15
r_work: 0.4076 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3958 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2223  Z= 0.167
  Angle     :  0.671   7.195   3017  Z= 0.354
  Chirality :  0.044   0.220    309
  Planarity :  0.005   0.049    384
  Dihedral  :  6.067  21.708    301
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.59 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.36 (0.51), residues: 122
  loop : -1.66 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1189 
 TYR   0.013   0.002   TYR H  95 
 PHE   0.009   0.001   PHE H  29 
 TRP   0.009   0.001   TRP A1197 
 HIS   0.004   0.002   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 2216)
  covalent geometry    : angle       0.66498 ( 3003)
  SS BOND              : bond        0.00455 (    7)
  SS BOND              : angle       1.48705 (   14)
  hydrogen bonds       : bond        0.03471 (   65)
  hydrogen bonds       : angle       6.78250 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: H   39 GLN cc_start: 0.7391 (pt0) cc_final: 0.6729 (tt0)
REVERT: L   81 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7157 (mt-10)
  outliers start: 2
  outliers final: 1
  residues processed: 40
  average time/residue: 0.5816
  time to fit residues: 23.7673
Evaluate side-chains
  38 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    0.3980
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 3 optimal weight:    0.1980
   chunk 9 optimal weight:    0.4980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.4340 r_free = 0.4340 target = 0.209439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.189483 restraints weight = 2485.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 2.11
r_work: 0.4079 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3961 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2223  Z= 0.150
  Angle     :  0.628   6.563   3017  Z= 0.331
  Chirality :  0.043   0.228    309
  Planarity :  0.005   0.052    384
  Dihedral  :  5.842  20.573    301
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.30 %
    Favored  : 84.98 %
  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 aren not related in a simple way.
  whole: -1.27 (0.53), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.00 (0.53), residues: 117
  loop : -1.57 (0.49), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  61 
 TYR   0.013   0.002   TYR H  95 
 PHE   0.006   0.001   PHE L  98 
 TRP   0.010   0.001   TRP A1197 
 HIS   0.004   0.001   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 2216)
  covalent geometry    : angle       0.62342 ( 3003)
  SS BOND              : bond        0.00414 (    7)
  SS BOND              : angle       1.22422 (   14)
  hydrogen bonds       : bond        0.03110 (   65)
  hydrogen bonds       : angle       6.55638 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: H   39 GLN cc_start: 0.7349 (pt0) cc_final: 0.6845 (tt0)
REVERT: L   81 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7563 (mm-30)
  outliers start: 4
  outliers final: 1
  residues processed: 40
  average time/residue: 0.6020
  time to fit residues: 24.5860
Evaluate side-chains
  37 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4319 r_free = 0.4319 target = 0.207228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.187254 restraints weight = 2449.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.4124 rms_B_bonded: 2.11
r_work: 0.4035 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3917 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   2223  Z= 0.203
  Angle     :  0.694   7.485   3017  Z= 0.367
  Chirality :  0.044   0.207    309
  Planarity :  0.005   0.058    384
  Dihedral  :  6.165  21.058    301
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.74 %
    Favored  : 80.69 %
  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 aren not related in a simple way.
  whole: -1.43 (0.53), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.27 (0.52), residues: 120
  loop : -1.55 (0.50), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  61 
 TYR   0.016   0.003   TYR A1358 
 PHE   0.008   0.002   PHE L  98 
 TRP   0.012   0.002   TRP A1197 
 HIS   0.005   0.002   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 2216)
  covalent geometry    : angle       0.68803 ( 3003)
  SS BOND              : bond        0.00483 (    7)
  SS BOND              : angle       1.46721 (   14)
  hydrogen bonds       : bond        0.03294 (   65)
  hydrogen bonds       : angle       6.96411 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.081 
Fit side-chains
REVERT: H   39 GLN cc_start: 0.7329 (pt0) cc_final: 0.7008 (tt0)
REVERT: H   80 TYR cc_start: 0.6096 (m-80) cc_final: 0.5612 (m-80)
REVERT: L   22 THR cc_start: 0.6806 (p) cc_final: 0.6590 (t)
REVERT: L   81 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7618 (mm-30)
  outliers start: 6
  outliers final: 2
  residues processed: 41
  average time/residue: 0.5812
  time to fit residues: 24.3717
Evaluate side-chains
  36 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 15 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0770
   chunk 3 optimal weight:    0.5980
   chunk 17 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.209600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.189886 restraints weight = 2472.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.4162 rms_B_bonded: 2.09
r_work: 0.4069 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3951 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2223  Z= 0.138
  Angle     :  0.630   7.267   3017  Z= 0.331
  Chirality :  0.043   0.239    309
  Planarity :  0.005   0.057    384
  Dihedral  :  5.712  20.662    301
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.03 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.53), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.29 (0.52), residues: 121
  loop : -1.51 (0.51), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  61 
 TYR   0.013   0.002   TYR H  95 
 PHE   0.006   0.001   PHE L  71 
 TRP   0.010   0.001   TRP A1197 
 HIS   0.005   0.001   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 2216)
  covalent geometry    : angle       0.62789 ( 3003)
  SS BOND              : bond        0.00371 (    7)
  SS BOND              : angle       0.95945 (   14)
  hydrogen bonds       : bond        0.02846 (   65)
  hydrogen bonds       : angle       6.46252 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.088 
Fit side-chains
REVERT: H   80 TYR cc_start: 0.6118 (m-80) cc_final: 0.5802 (m-80)
REVERT: L   81 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7564 (mm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 39
  average time/residue: 0.5435
  time to fit residues: 21.6852
Evaluate side-chains
  36 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0010
   chunk 2 optimal weight:    0.0970
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.3584

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

Flipped N/Q/H residues before XYZ refinement:
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.210486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.191194 restraints weight = 2372.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.4179 rms_B_bonded: 2.01
r_work: 0.4085 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3969 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2223  Z= 0.138
  Angle     :  0.649   7.213   3017  Z= 0.338
  Chirality :  0.043   0.222    309
  Planarity :  0.005   0.057    384
  Dihedral  :  5.699  20.342    301
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.88 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.53), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.26 (0.52), residues: 120
  loop : -1.51 (0.51), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  61 
 TYR   0.011   0.002   TYR H 102 
 PHE   0.006   0.001   PHE H 106 
 TRP   0.010   0.001   TRP A1197 
 HIS   0.004   0.001   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 2216)
  covalent geometry    : angle       0.64359 ( 3003)
  SS BOND              : bond        0.00350 (    7)
  SS BOND              : angle       1.40495 (   14)
  hydrogen bonds       : bond        0.02763 (   65)
  hydrogen bonds       : angle       6.31981 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A 1359 TYR cc_start: 0.7693 (p90) cc_final: 0.7449 (p90)
REVERT: H   80 TYR cc_start: 0.6093 (m-80) cc_final: 0.5776 (m-80)
REVERT: L   81 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7588 (mm-30)
  outliers start: 6
  outliers final: 2
  residues processed: 39
  average time/residue: 0.5723
  time to fit residues: 22.8148
Evaluate side-chains
  38 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0060
   chunk 25 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0970
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.3594

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

Flipped N/Q/H residues before XYZ refinement:
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.211002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.191450 restraints weight = 2428.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.4195 rms_B_bonded: 2.04
r_work: 0.4099 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3977 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2223  Z= 0.137
  Angle     :  0.644   7.149   3017  Z= 0.335
  Chirality :  0.043   0.233    309
  Planarity :  0.005   0.058    384
  Dihedral  :  5.558  20.215    301
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 19.74 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.53), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.30 (0.51), residues: 121
  loop : -1.52 (0.50), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  24 
 TYR   0.011   0.002   TYR H 102 
 PHE   0.007   0.001   PHE H 106 
 TRP   0.010   0.001   TRP A1197 
 HIS   0.004   0.001   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 2216)
  covalent geometry    : angle       0.63938 ( 3003)
  SS BOND              : bond        0.00346 (    7)
  SS BOND              : angle       1.34487 (   14)
  hydrogen bonds       : bond        0.02730 (   65)
  hydrogen bonds       : angle       6.25588 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A 1359 TYR cc_start: 0.7688 (p90) cc_final: 0.7421 (p90)
REVERT: H   80 TYR cc_start: 0.6099 (m-80) cc_final: 0.5782 (m-80)
REVERT: L   81 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7580 (mm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 38
  average time/residue: 0.5211
  time to fit residues: 20.2799
Evaluate side-chains
  37 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.207114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.187074 restraints weight = 2436.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 2.08
r_work: 0.4044 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3927 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   2223  Z= 0.208
  Angle     :  0.718   7.597   3017  Z= 0.375
  Chirality :  0.044   0.199    309
  Planarity :  0.006   0.068    384
  Dihedral  :  5.993  20.491    301
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 20.17 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.34 (0.51), residues: 120
  loop : -1.57 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  98 
 TYR   0.016   0.003   TYR H 102 
 PHE   0.010   0.002   PHE H 106 
 TRP   0.013   0.002   TRP A1197 
 HIS   0.005   0.002   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 2216)
  covalent geometry    : angle       0.71107 ( 3003)
  SS BOND              : bond        0.00482 (    7)
  SS BOND              : angle       1.58485 (   14)
  hydrogen bonds       : bond        0.03117 (   65)
  hydrogen bonds       : angle       6.77384 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.083 
Fit side-chains
REVERT: H   65 LYS cc_start: 0.7292 (pttt) cc_final: 0.7056 (pttp)
REVERT: H   80 TYR cc_start: 0.6190 (m-80) cc_final: 0.5907 (m-80)
REVERT: L   81 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7471 (mt-10)
  outliers start: 5
  outliers final: 2
  residues processed: 39
  average time/residue: 0.3929
  time to fit residues: 15.7004
Evaluate side-chains
  38 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0980
   chunk 3 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0980
   chunk 16 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 6 optimal weight:    0.3980
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.3380

-------------------------------------------------------------------------------
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 = 0.4360 r_free = 0.4360 target = 0.210837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.190608 restraints weight = 2433.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.4173 rms_B_bonded: 2.13
r_work: 0.4080 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3958 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2223  Z= 0.135
  Angle     :  0.655   7.103   3017  Z= 0.339
  Chirality :  0.043   0.232    309
  Planarity :  0.005   0.059    384
  Dihedral  :  5.589  20.418    301
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 20.17 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.32 (0.51), residues: 121
  loop : -1.58 (0.49), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  24 
 TYR   0.011   0.002   TYR L  92 
 PHE   0.007   0.001   PHE H 106 
 TRP   0.011   0.001   TRP A1197 
 HIS   0.005   0.001   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 2216)
  covalent geometry    : angle       0.65122 ( 3003)
  SS BOND              : bond        0.00339 (    7)
  SS BOND              : angle       1.22922 (   14)
  hydrogen bonds       : bond        0.02734 (   65)
  hydrogen bonds       : angle       6.27915 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.053 
Fit side-chains
REVERT: A 1359 TYR cc_start: 0.7732 (p90) cc_final: 0.7454 (p90)
REVERT: H   65 LYS cc_start: 0.7093 (pttt) cc_final: 0.6870 (pttp)
REVERT: H   80 TYR cc_start: 0.6140 (m-80) cc_final: 0.5852 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 35
  average time/residue: 0.4250
  time to fit residues: 15.1970
Evaluate side-chains
  33 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0570
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.4351 r_free = 0.4351 target = 0.209913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.190200 restraints weight = 2457.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.4153 rms_B_bonded: 2.05
r_work: 0.4063 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3943 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2223  Z= 0.180
  Angle     :  0.712   8.682   3017  Z= 0.369
  Chirality :  0.044   0.215    309
  Planarity :  0.005   0.061    384
  Dihedral  :  5.796  20.517    301
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 21.03 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.52 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.34 (0.51), residues: 120
  loop : -1.61 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  61 
 TYR   0.016   0.002   TYR H  94 
 PHE   0.013   0.001   PHE H 106 
 TRP   0.012   0.002   TRP A1197 
 HIS   0.005   0.002   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 2216)
  covalent geometry    : angle       0.70733 ( 3003)
  SS BOND              : bond        0.00417 (    7)
  SS BOND              : angle       1.39871 (   14)
  hydrogen bonds       : bond        0.02959 (   65)
  hydrogen bonds       : angle       6.58628 (  165)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.050 
Fit side-chains
REVERT: A 1359 TYR cc_start: 0.7715 (p90) cc_final: 0.7427 (p90)
REVERT: H   65 LYS cc_start: 0.7236 (pttt) cc_final: 0.7026 (pttp)
REVERT: H   80 TYR cc_start: 0.6164 (m-80) cc_final: 0.5888 (m-80)
  outliers start: 2
  outliers final: 2
  residues processed: 35
  average time/residue: 0.3327
  time to fit residues: 11.9510
Evaluate side-chains
  33 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0570
   chunk 25 optimal weight:    0.0050
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.3912

-------------------------------------------------------------------------------
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 = 0.4355 r_free = 0.4355 target = 0.210155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.189887 restraints weight = 2479.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.4169 rms_B_bonded: 2.14
r_work: 0.4076 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3955 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2223  Z= 0.147
  Angle     :  0.680   8.747   3017  Z= 0.350
  Chirality :  0.043   0.225    309
  Planarity :  0.005   0.058    384
  Dihedral  :  5.597  20.264    301
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 21.03 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet: -0.33 (0.51), residues: 121
  loop : -1.55 (0.49), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  61 
 TYR   0.012   0.002   TYR H  94 
 PHE   0.010   0.001   PHE H 106 
 TRP   0.012   0.001   TRP A1197 
 HIS   0.005   0.001   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2216)
  covalent geometry    : angle       0.67613 ( 3003)
  SS BOND              : bond        0.00346 (    7)
  SS BOND              : angle       1.24797 (   14)
  hydrogen bonds       : bond        0.02763 (   65)
  hydrogen bonds       : angle       6.35564 (  165)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1060.63 seconds
wall clock time: 20 minutes 20.91 seconds (1220.91 seconds total)