Starting phenix.real_space_refine
on Wed Sep 17 03:21:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jaz_61302/09_2025/9jaz_61302.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jaz_61302/09_2025/9jaz_61302.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jaz_61302/09_2025/9jaz_61302.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jaz_61302/09_2025/9jaz_61302.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jaz_61302/09_2025/9jaz_61302.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jaz_61302/09_2025/9jaz_61302.map"
  }
  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=   0.001
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      12      5.16       5
     C    1956      2.51       5
     N     504      2.21       5
     O     540      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3012
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "F"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 121
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
    Chain: "F"
      Number of atoms: 130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 130
          Classifications: {'peptide': 20}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 19}
  Restraints were copied for chains:
    E, D, C, B, A, FF, EE, DD, CC, BB, AA
  Time building chain proxies: 0.56, per 1000 atoms: 0.19
  Number of scatterers: 3012
  At special positions: 0
  Unit cell: (68.89, 73.87, 44.82, 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      12     16.00
     O     540      8.00
     N     504      7.00
     C    1956      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Links applied
    TRANS
      " DAS A  23 " - " GLU A  22 "
      " DAS B  23 " - " GLU B  22 "
      " DAS C  23 " - " GLU C  22 "
      " DAS D  23 " - " GLU D  22 "
      " DAS E  23 " - " GLU E  22 "
      " DAS F  23 " - " GLU F  22 "
      " DASAA  23 " - " GLUAA  22 "
      " DASBB  23 " - " GLUBB  22 "
      " DASCC  23 " - " GLUCC  22 "
      " DASDD  23 " - " GLUDD  22 "
      " DASEE  23 " - " GLUEE  22 "
      " DASFF  23 " - " GLUFF  22 "
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 111.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAS F  23 "
        pdb=" CB  DAS E  23 "
        pdb=" CB  DAS D  23 "
        pdb=" CB  DAS C  23 "
        pdb=" CB  DAS B  23 "
        pdb=" CB  DAS A  23 "
        pdb=" CB  DASFF  23 "
        pdb=" CB  DASEE  23 "
        pdb=" CB  DASDD  23 "
        pdb=" CB  DASCC  23 "
        pdb=" CB  DASBB  23 "
        pdb=" CB  DASAA  23 "
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 42.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'F' and resid 10 through 13
    Processing sheet with id=AA2, first strand: chain 'F' and resid 15 through 20
    Processing sheet with id=AA3, first strand: chain 'F' and resid 30 through 32
      removed outlier: 6.674A  pdb=" N   ALA F  30 " --> pdb=" O   ILE E  31 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ALA E  30 " --> pdb=" O   ILE D  31 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ALA D  30 " --> pdb=" O   ILE C  31 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ALA C  30 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ALA B  30 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'F' and resid 34 through 36
      removed outlier: 8.983A  pdb=" N   LEU F  34 " --> pdb=" O   MET E  35 " (cutoff:3.500A)
      removed outlier: 8.990A  pdb=" N   LEU E  34 " --> pdb=" O   MET D  35 " (cutoff:3.500A)
      removed outlier: 9.009A  pdb=" N   LEU D  34 " --> pdb=" O   MET C  35 " (cutoff:3.500A)
      removed outlier: 9.005A  pdb=" N   LEU C  34 " --> pdb=" O   MET B  35 " (cutoff:3.500A)
      removed outlier: 8.989A  pdb=" N   LEU B  34 " --> pdb=" O   MET A  35 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 39 through 41
      removed outlier: 6.082A  pdb=" N   VAL F  39 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   VAL E  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   VAL D  39 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   VAL C  39 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   VAL B  39 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'FF' and resid 10 through 13
    Processing sheet with id=AA7, first strand: chain 'FF' and resid 15 through 20
    Processing sheet with id=AA8, first strand: chain 'FF' and resid 30 through 32
      removed outlier: 6.642A  pdb=" N   ALAFF  30 " --> pdb=" O   ILEEE  31 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ALAEE  30 " --> pdb=" O   ILEDD  31 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ALADD  30 " --> pdb=" O   ILECC  31 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ALACC  30 " --> pdb=" O   ILEBB  31 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ALABB  30 " --> pdb=" O   ILEAA  31 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'FF' and resid 34 through 36
      removed outlier: 9.004A  pdb=" N   LEUFF  34 " --> pdb=" O   METEE  35 " (cutoff:3.500A)
      removed outlier: 8.970A  pdb=" N   LEUEE  34 " --> pdb=" O   METDD  35 " (cutoff:3.500A)
      removed outlier: 8.997A  pdb=" N   LEUDD  34 " --> pdb=" O   METCC  35 " (cutoff:3.500A)
      removed outlier: 9.028A  pdb=" N   LEUCC  34 " --> pdb=" O   METBB  35 " (cutoff:3.500A)
      removed outlier: 8.980A  pdb=" N   LEUBB  34 " --> pdb=" O   METAA  35 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AA10, first strand: chain 'FF' and resid 39 through 41
      removed outlier: 6.121A  pdb=" N   VALFF  39 " --> pdb=" O   VALEE  40 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   VALEE  39 " --> pdb=" O   VALDD  40 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   VALDD  39 " --> pdb=" O   VALCC  40 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VALCC  39 " --> pdb=" O   VALBB  40 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VALBB  39 " --> pdb=" O   VALAA  40 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA10

    80 hydrogen bonds defined for protein.
    240 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: 0.44

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 972
        1.34 -     1.45: 384
        1.45 -     1.57: 1668
        1.57 -     1.68: 0
        1.68 -     1.79: 24
  Bond restraints: 3048
  Sorted by residual:
  bond pdb=" C   VALFF  36 "
       pdb=" N   GLYFF  37 "
    ideal  model  delta    sigma   weight residual
    1.327  1.320  0.007 1.11e-02 8.12e+03 3.86e-01
  bond pdb=" C   VAL F  36 "
       pdb=" N   GLY F  37 "
    ideal  model  delta    sigma   weight residual
    1.327  1.320  0.007 1.11e-02 8.12e+03 3.70e-01
  bond pdb=" C   VALEE  36 "
       pdb=" N   GLYEE  37 "
    ideal  model  delta    sigma   weight residual
    1.327  1.320  0.007 1.11e-02 8.12e+03 3.49e-01
  bond pdb=" C   VALDD  36 "
       pdb=" N   GLYDD  37 "
    ideal  model  delta    sigma   weight residual
    1.327  1.320  0.007 1.11e-02 8.12e+03 3.47e-01
  bond pdb=" C   VALCC  36 "
       pdb=" N   GLYCC  37 "
    ideal  model  delta    sigma   weight residual
    1.327  1.320  0.006 1.11e-02 8.12e+03 3.34e-01
  ... (remaining 3043 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.62: 3492
        0.62 -     1.25: 430
        1.25 -     1.87: 98
        1.87 -     2.50: 36
        2.50 -     3.12: 24
  Bond angle restraints: 4080
  Sorted by residual:
  angle pdb=" C   SER D  26 "
        pdb=" CA  SER D  26 "
        pdb=" CB  SER D  26 "
      ideal   model   delta    sigma   weight residual
     111.89  109.85    2.04 1.42e+00 4.96e-01 2.06e+00
  angle pdb=" C   SERBB  26 "
        pdb=" CA  SERBB  26 "
        pdb=" CB  SERBB  26 "
      ideal   model   delta    sigma   weight residual
     111.89  109.85    2.04 1.42e+00 4.96e-01 2.06e+00
  angle pdb=" C   SER C  26 "
        pdb=" CA  SER C  26 "
        pdb=" CB  SER C  26 "
      ideal   model   delta    sigma   weight residual
     111.89  109.86    2.03 1.42e+00 4.96e-01 2.05e+00
  angle pdb=" N   GLYAA  25 "
        pdb=" CA  GLYAA  25 "
        pdb=" C   GLYAA  25 "
      ideal   model   delta    sigma   weight residual
     111.31  114.08   -2.77 1.95e+00 2.63e-01 2.02e+00
  angle pdb=" N   GLYDD  25 "
        pdb=" CA  GLYDD  25 "
        pdb=" C   GLYDD  25 "
      ideal   model   delta    sigma   weight residual
     111.31  114.07   -2.76 1.95e+00 2.63e-01 2.01e+00
  ... (remaining 4075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.28: 1381
       11.28 -    22.55: 155
       22.55 -    33.83: 96
       33.83 -    45.10: 48
       45.10 -    56.37: 24
  Dihedral angle restraints: 1704
    sinusoidal: 648
      harmonic: 1056
  Sorted by residual:
  dihedral pdb=" CA  LEUAA  17 "
           pdb=" CB  LEUAA  17 "
           pdb=" CG  LEUAA  17 "
           pdb=" CD1 LEUAA  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  138.50   41.50     3      1.50e+01 4.44e-03 7.43e+00
  dihedral pdb=" CA  LEUFF  17 "
           pdb=" CB  LEUFF  17 "
           pdb=" CG  LEUFF  17 "
           pdb=" CD1 LEUFF  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  138.51   41.49     3      1.50e+01 4.44e-03 7.42e+00
  dihedral pdb=" CA  LEU A  17 "
           pdb=" CB  LEU A  17 "
           pdb=" CG  LEU A  17 "
           pdb=" CD1 LEU A  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  138.51   41.49     3      1.50e+01 4.44e-03 7.42e+00
  ... (remaining 1701 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 216
       0.026 -    0.051: 134
       0.051 -    0.076: 22
       0.076 -    0.102: 32
       0.102 -    0.127: 64
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CA  VALEE  12 "
            pdb=" N   VALEE  12 "
            pdb=" C   VALEE  12 "
            pdb=" CB  VALEE  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.05e-01
  chirality pdb=" CA  VAL D  12 "
            pdb=" N   VAL D  12 "
            pdb=" C   VAL D  12 "
            pdb=" CB  VAL D  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.05e-01
  chirality pdb=" CA  VAL F  12 "
            pdb=" N   VAL F  12 "
            pdb=" C   VAL F  12 "
            pdb=" CB  VAL F  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 465 not shown)

  Planarity restraints: 528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS F  13 "   -0.003 2.00e-02 2.50e+03   5.43e-03 2.95e-01
        pdb=" C   HIS F  13 "    0.009 2.00e-02 2.50e+03
        pdb=" O   HIS F  13 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   HIS F  14 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A  13 "   -0.003 2.00e-02 2.50e+03   5.41e-03 2.93e-01
        pdb=" C   HIS A  13 "    0.009 2.00e-02 2.50e+03
        pdb=" O   HIS A  13 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   HIS A  14 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HISFF  13 "    0.003 2.00e-02 2.50e+03   5.34e-03 2.86e-01
        pdb=" C   HISFF  13 "   -0.009 2.00e-02 2.50e+03
        pdb=" O   HISFF  13 "    0.004 2.00e-02 2.50e+03
        pdb=" N   HISFF  14 "    0.003 2.00e-02 2.50e+03
  ... (remaining 525 not shown)

  Histogram of nonbonded interaction distances:
        2.62 -     3.08: 1949
        3.08 -     3.53: 2807
        3.53 -     3.99: 4789
        3.99 -     4.44: 5730
        4.44 -     4.90: 10681
  Nonbonded interactions: 25956
  Sorted by model distance:
  nonbonded pdb=" O   DASEE  23 "
            pdb=" N   VALDD  24 "
     model   vdw
     2.622 3.120
  nonbonded pdb=" O   DASBB  23 "
            pdb=" N   VALAA  24 "
     model   vdw
     2.636 3.120
  nonbonded pdb=" O   DAS E  23 "
            pdb=" N   VAL D  24 "
     model   vdw
     2.649 3.120
  nonbonded pdb=" O   DAS F  23 "
            pdb=" N   VAL E  24 "
     model   vdw
     2.649 3.120
  nonbonded pdb=" O   DASFF  23 "
            pdb=" N   VALEE  24 "
     model   vdw
     2.660 3.120
  ... (remaining 25951 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 'F'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'A'
  selection = chain 'FF'
  selection = chain 'EE'
  selection = chain 'DD'
  selection = chain 'CC'
  selection = chain 'BB'
  selection = chain 'AA'
}

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:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.470
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
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      :  0.004   0.019   3060  Z= 0.168
  Angle     :  0.522   3.123   4116  Z= 0.309
  Chirality :  0.054   0.127    468
  Planarity :  0.001   0.005    516
  Dihedral  : 15.936  56.374   1020
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 33.33 %
    Favored  : 66.67 %
  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 aren not related in a simple way.
  whole: -0.70 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.53 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR C  10 
 PHE   0.007   0.002   PHE B  20 
 HIS   0.003   0.002   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 3048)
  covalent geometry    : angle       0.52464 ( 4080)
  hydrogen bonds       : bond        0.13977 (   80)
  hydrogen bonds       : angle       8.03712 (  240)
  link_TRANS           : bond        0.00097 (   12)
  link_TRANS           : angle       0.12721 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.094 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8573 (mtpm) cc_final: 0.8160 (mttp)
REVERT: C   28 LYS cc_start: 0.8500 (mtpm) cc_final: 0.8093 (mttp)
REVERT: B   28 LYS cc_start: 0.8506 (mtpm) cc_final: 0.8018 (mttp)
REVERT: A   28 LYS cc_start: 0.8891 (mtpm) cc_final: 0.8510 (mttm)
REVERT: EE   28 LYS cc_start: 0.8628 (mtpm) cc_final: 0.8393 (mtpt)
REVERT: DD   28 LYS cc_start: 0.8526 (mtpm) cc_final: 0.8158 (mttm)
REVERT: CC   28 LYS cc_start: 0.8483 (mtpm) cc_final: 0.8105 (mttp)
REVERT: BB   28 LYS cc_start: 0.8374 (mtpm) cc_final: 0.7865 (mttp)
REVERT: AA   28 LYS cc_start: 0.8861 (mtpm) cc_final: 0.8421 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.9281
  time to fit residues: 22.6923
Evaluate side-chains
  24 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0040
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0040
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.7606

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.117822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.082184 restraints weight = 3341.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.97
r_work: 0.3243 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.0823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   3060  Z= 0.158
  Angle     :  0.471   4.851   4116  Z= 0.263
  Chirality :  0.058   0.126    468
  Planarity :  0.002   0.007    516
  Dihedral  :  4.777  13.466    432
  Min Nonbonded Distance : 2.695

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 31.94 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.60 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR F  10 
 PHE   0.009   0.002   PHE A  20 
 HIS   0.005   0.002   HISDD  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3048)
  covalent geometry    : angle       0.47251 ( 4080)
  hydrogen bonds       : bond        0.03535 (   80)
  hydrogen bonds       : angle       5.01135 (  240)
  link_TRANS           : bond        0.00084 (   12)
  link_TRANS           : angle       0.11937 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.108 
Fit side-chains
REVERT: F   28 LYS cc_start: 0.8026 (mtpm) cc_final: 0.7653 (mtpp)
REVERT: D   28 LYS cc_start: 0.8133 (mtpm) cc_final: 0.7661 (mttp)
REVERT: C   28 LYS cc_start: 0.8172 (mtpm) cc_final: 0.7673 (mttp)
REVERT: B   28 LYS cc_start: 0.8264 (mtpm) cc_final: 0.7706 (mttp)
REVERT: A   28 LYS cc_start: 0.8638 (mtpm) cc_final: 0.8204 (mttm)
REVERT: DD   28 LYS cc_start: 0.8076 (mtpm) cc_final: 0.7596 (mttm)
REVERT: CC   28 LYS cc_start: 0.8105 (mtpm) cc_final: 0.7676 (mttp)
REVERT: BB   28 LYS cc_start: 0.8096 (mtpm) cc_final: 0.7536 (mttp)
REVERT: AA   28 LYS cc_start: 0.8564 (mtpm) cc_final: 0.7925 (mttp)
  outliers start: 5
  outliers final: 3
  residues processed: 26
  average time/residue: 0.8211
  time to fit residues: 21.8409
Evaluate side-chains
  27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain DD residue   35 MET
Chi-restraints excluded: chain CC residue   39 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0040
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.9396

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.118513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.082657 restraints weight = 3410.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 3.06
r_work: 0.3197 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3060  Z= 0.184
  Angle     :  0.477   4.595   4116  Z= 0.270
  Chirality :  0.057   0.127    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.033  15.139    432
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 30.56 %
    Favored  : 65.28 %
  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: -0.79 (0.45), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.59 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYRCC  10 
 PHE   0.011   0.002   PHE A  20 
 HIS   0.005   0.002   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 3048)
  covalent geometry    : angle       0.47923 ( 4080)
  hydrogen bonds       : bond        0.03288 (   80)
  hydrogen bonds       : angle       4.79143 (  240)
  link_TRANS           : bond        0.00070 (   12)
  link_TRANS           : angle       0.14424 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 0.115 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8130 (mtpm) cc_final: 0.7662 (mttp)
REVERT: C   28 LYS cc_start: 0.8138 (mtpm) cc_final: 0.7614 (mttp)
REVERT: B   28 LYS cc_start: 0.8243 (mtpm) cc_final: 0.7712 (mttp)
REVERT: A   28 LYS cc_start: 0.8637 (mtpm) cc_final: 0.8223 (mttp)
REVERT: FF   35 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7596 (ttt)
REVERT: DD   28 LYS cc_start: 0.8097 (mtpm) cc_final: 0.7602 (mttp)
REVERT: CC   28 LYS cc_start: 0.8043 (mtpm) cc_final: 0.7614 (mttp)
REVERT: BB   28 LYS cc_start: 0.8101 (mtpm) cc_final: 0.7519 (mttp)
REVERT: AA   28 LYS cc_start: 0.8536 (mtpm) cc_final: 0.7909 (mttp)
  outliers start: 12
  outliers final: 3
  residues processed: 29
  average time/residue: 0.7835
  time to fit residues: 23.2445
Evaluate side-chains
  28 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain DD residue   35 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.117352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.080803 restraints weight = 3433.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 3.09
r_work: 0.3175 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3060  Z= 0.200
  Angle     :  0.492   5.322   4116  Z= 0.278
  Chirality :  0.058   0.126    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.188  16.597    432
  Min Nonbonded Distance : 2.688

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 30.90 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.61 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR D  10 
 PHE   0.011   0.002   PHE A  20 
 HIS   0.005   0.002   HISDD  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 3048)
  covalent geometry    : angle       0.49395 ( 4080)
  hydrogen bonds       : bond        0.03077 (   80)
  hydrogen bonds       : angle       4.72301 (  240)
  link_TRANS           : bond        0.00084 (   12)
  link_TRANS           : angle       0.15874 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 24
  time to evaluate  : 0.115 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8219 (mtpm) cc_final: 0.7751 (mttp)
REVERT: C   28 LYS cc_start: 0.8252 (mtpm) cc_final: 0.7744 (mttp)
REVERT: B   28 LYS cc_start: 0.8366 (mtpm) cc_final: 0.7837 (mttp)
REVERT: A   28 LYS cc_start: 0.8757 (mtpm) cc_final: 0.8343 (mttp)
REVERT: FF   35 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7721 (ttm)
REVERT: DD   28 LYS cc_start: 0.8170 (mtpm) cc_final: 0.7695 (mttp)
REVERT: CC   28 LYS cc_start: 0.8131 (mtpm) cc_final: 0.7701 (mttp)
REVERT: BB   28 LYS cc_start: 0.8260 (mtpm) cc_final: 0.7689 (mttp)
REVERT: AA   28 LYS cc_start: 0.8633 (mtpm) cc_final: 0.8015 (mttp)
  outliers start: 10
  outliers final: 2
  residues processed: 28
  average time/residue: 0.7853
  time to fit residues: 22.5034
Evaluate side-chains
  27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain DD residue   35 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.120972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.083642 restraints weight = 3320.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 3.11
r_work: 0.3241 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3060  Z= 0.132
  Angle     :  0.446   5.354   4116  Z= 0.251
  Chirality :  0.057   0.126    468
  Planarity :  0.002   0.007    516
  Dihedral  :  4.950  15.240    432
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 30.90 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.62 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYRDD  10 
 PHE   0.008   0.002   PHE C  19 
 HIS   0.004   0.002   HISDD  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3048)
  covalent geometry    : angle       0.44760 ( 4080)
  hydrogen bonds       : bond        0.02777 (   80)
  hydrogen bonds       : angle       4.65726 (  240)
  link_TRANS           : bond        0.00030 (   12)
  link_TRANS           : angle       0.20154 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 24
  time to evaluate  : 0.111 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8063 (mtpm) cc_final: 0.7581 (mttp)
REVERT: C   28 LYS cc_start: 0.8049 (mtpm) cc_final: 0.7540 (mttp)
REVERT: B   28 LYS cc_start: 0.8191 (mtpm) cc_final: 0.7639 (mttp)
REVERT: A   28 LYS cc_start: 0.8581 (mtpm) cc_final: 0.8166 (mttp)
REVERT: FF   35 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7187 (ttm)
REVERT: DD   28 LYS cc_start: 0.8002 (mtpm) cc_final: 0.7503 (mttp)
REVERT: CC   28 LYS cc_start: 0.7925 (mtpm) cc_final: 0.7476 (mttp)
REVERT: BB   28 LYS cc_start: 0.8121 (mtpm) cc_final: 0.7524 (mttp)
REVERT: AA   28 LYS cc_start: 0.8484 (mtpm) cc_final: 0.7836 (mttp)
REVERT: AA   35 MET cc_start: 0.8710 (ttp) cc_final: 0.8330 (tpp)
  outliers start: 10
  outliers final: 1
  residues processed: 27
  average time/residue: 0.8468
  time to fit residues: 23.3551
Evaluate side-chains
  26 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain DD residue   35 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    1.9188

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.113160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.077449 restraints weight = 3437.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 3.07
r_work: 0.3127 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.043   3060  Z= 0.335
  Angle     :  0.609   5.615   4116  Z= 0.340
  Chirality :  0.060   0.133    468
  Planarity :  0.003   0.008    516
  Dihedral  :  5.539  21.005    432
  Min Nonbonded Distance : 2.682

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 29.51 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.55 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR E  10 
 PHE   0.015   0.003   PHE C  19 
 HIS   0.007   0.003   HISDD  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00801 ( 3048)
  covalent geometry    : angle       0.61165 ( 4080)
  hydrogen bonds       : bond        0.03428 (   80)
  hydrogen bonds       : angle       4.70237 (  240)
  link_TRANS           : bond        0.00170 (   12)
  link_TRANS           : angle       0.19733 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.115 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8184 (mtpm) cc_final: 0.7695 (mttp)
REVERT: C   28 LYS cc_start: 0.8185 (mtpm) cc_final: 0.7668 (mttp)
REVERT: B   28 LYS cc_start: 0.8353 (mtpm) cc_final: 0.7801 (mttp)
REVERT: A   28 LYS cc_start: 0.8722 (mtpm) cc_final: 0.8268 (mttm)
REVERT: FF   35 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7451 (ttt)
REVERT: DD   28 LYS cc_start: 0.8112 (mtpm) cc_final: 0.7646 (mttp)
REVERT: CC   17 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8071 (tt)
REVERT: CC   28 LYS cc_start: 0.8086 (mtpm) cc_final: 0.7598 (mttp)
REVERT: BB   28 LYS cc_start: 0.8255 (mtpm) cc_final: 0.7671 (mttp)
REVERT: AA   28 LYS cc_start: 0.8650 (mtpm) cc_final: 0.8073 (mttp)
REVERT: AA   35 MET cc_start: 0.8936 (ttp) cc_final: 0.8704 (tpp)
  outliers start: 14
  outliers final: 5
  residues processed: 31
  average time/residue: 0.7036
  time to fit residues: 22.3442
Evaluate side-chains
  31 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain FF residue   28 LYS
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain DD residue   35 MET
Chi-restraints excluded: chain DD residue   39 VAL
Chi-restraints excluded: chain CC residue   17 LEU
Chi-restraints excluded: chain CC residue   39 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    0.2980
   chunk 21 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   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 = 0.3934 r_free = 0.3934 target = 0.119947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.084251 restraints weight = 3330.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 3.01
r_work: 0.3250 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3060  Z= 0.140
  Angle     :  0.466   5.675   4116  Z= 0.261
  Chirality :  0.058   0.127    468
  Planarity :  0.002   0.007    516
  Dihedral  :  4.986  19.398    432
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 30.21 %
    Favored  : 65.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.56 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYRDD  10 
 PHE   0.008   0.002   PHE A  20 
 HIS   0.005   0.002   HISDD  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3048)
  covalent geometry    : angle       0.46780 ( 4080)
  hydrogen bonds       : bond        0.02809 (   80)
  hydrogen bonds       : angle       4.68172 (  240)
  link_TRANS           : bond        0.00035 (   12)
  link_TRANS           : angle       0.23651 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 24
  time to evaluate  : 0.114 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8218 (mtpm) cc_final: 0.7730 (mttp)
REVERT: C   28 LYS cc_start: 0.8205 (mtpm) cc_final: 0.7712 (mttp)
REVERT: B   28 LYS cc_start: 0.8305 (mtpm) cc_final: 0.7774 (mttp)
REVERT: A   28 LYS cc_start: 0.8692 (mtpm) cc_final: 0.8286 (mttp)
REVERT: FF   35 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7269 (ttm)
REVERT: DD   28 LYS cc_start: 0.8138 (mtpm) cc_final: 0.7628 (mttp)
REVERT: CC   17 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8016 (tt)
REVERT: CC   28 LYS cc_start: 0.8070 (mtpm) cc_final: 0.7626 (mttp)
REVERT: BB   28 LYS cc_start: 0.8233 (mtpm) cc_final: 0.7639 (mttp)
REVERT: AA   28 LYS cc_start: 0.8599 (mtpm) cc_final: 0.8094 (mttp)
  outliers start: 11
  outliers final: 1
  residues processed: 29
  average time/residue: 0.7676
  time to fit residues: 22.7360
Evaluate side-chains
  27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain CC residue   17 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0570
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.1304

-------------------------------------------------------------------------------
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 = 0.3888 r_free = 0.3888 target = 0.116043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.080333 restraints weight = 3397.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 3.04
r_work: 0.3189 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3060  Z= 0.212
  Angle     :  0.525   5.897   4116  Z= 0.292
  Chirality :  0.058   0.127    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.202  20.309    432
  Min Nonbonded Distance : 2.683

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 30.21 %
    Favored  : 64.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.78 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.58 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR D  10 
 PHE   0.011   0.003   PHE C  19 
 HIS   0.007   0.003   HISDD  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 3048)
  covalent geometry    : angle       0.52750 ( 4080)
  hydrogen bonds       : bond        0.03119 (   80)
  hydrogen bonds       : angle       4.68341 (  240)
  link_TRANS           : bond        0.00068 (   12)
  link_TRANS           : angle       0.18722 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.133 
Fit side-chains
REVERT: D   17 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8143 (tt)
REVERT: D   28 LYS cc_start: 0.8266 (mtpm) cc_final: 0.7781 (mttp)
REVERT: C   28 LYS cc_start: 0.8259 (mtpm) cc_final: 0.7809 (mttp)
REVERT: B   28 LYS cc_start: 0.8392 (mtpm) cc_final: 0.7833 (mttp)
REVERT: A   28 LYS cc_start: 0.8764 (mtpm) cc_final: 0.8351 (mttm)
REVERT: FF   35 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7592 (ttt)
REVERT: DD   28 LYS cc_start: 0.8201 (mtpm) cc_final: 0.7732 (mttp)
REVERT: CC   28 LYS cc_start: 0.8197 (mtpm) cc_final: 0.7763 (mttp)
REVERT: BB   28 LYS cc_start: 0.8310 (mtpm) cc_final: 0.7723 (mttp)
REVERT: AA   28 LYS cc_start: 0.8679 (mtpm) cc_final: 0.8086 (mttp)
  outliers start: 14
  outliers final: 3
  residues processed: 31
  average time/residue: 0.7107
  time to fit residues: 22.5688
Evaluate side-chains
  29 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain DD residue   35 MET
Chi-restraints excluded: chain CC residue   39 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 26 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0770
   chunk 19 optimal weight:    0.0370
   overall best weight:    0.3816

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.122760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.084876 restraints weight = 3227.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 3.07
r_work: 0.3304 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3060  Z= 0.097
  Angle     :  0.457   5.994   4116  Z= 0.247
  Chirality :  0.058   0.126    468
  Planarity :  0.001   0.007    516
  Dihedral  :  4.784  18.437    432
  Min Nonbonded Distance : 2.694

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 31.60 %
    Favored  : 65.28 %
  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: -0.80 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.60 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR D  10 
 PHE   0.006   0.002   PHE D  20 
 HIS   0.004   0.001   HISDD  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 3048)
  covalent geometry    : angle       0.45763 ( 4080)
  hydrogen bonds       : bond        0.02678 (   80)
  hydrogen bonds       : angle       4.61384 (  240)
  link_TRANS           : bond        0.00031 (   12)
  link_TRANS           : angle       0.34832 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 24
  time to evaluate  : 0.112 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8053 (mtpm) cc_final: 0.7565 (mttp)
REVERT: C   28 LYS cc_start: 0.8028 (mtpm) cc_final: 0.7568 (mttp)
REVERT: B   28 LYS cc_start: 0.8175 (mtpm) cc_final: 0.7602 (mttp)
REVERT: A   28 LYS cc_start: 0.8462 (mtpm) cc_final: 0.8053 (mttm)
REVERT: FF   35 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7107 (ttm)
REVERT: DD   28 LYS cc_start: 0.7938 (mtpm) cc_final: 0.7408 (mttp)
REVERT: CC   28 LYS cc_start: 0.7895 (mtpm) cc_final: 0.7419 (mttp)
REVERT: BB   28 LYS cc_start: 0.8060 (mtpm) cc_final: 0.7523 (mtmm)
REVERT: AA   28 LYS cc_start: 0.8426 (mtpm) cc_final: 0.7974 (mttp)
  outliers start: 9
  outliers final: 1
  residues processed: 27
  average time/residue: 0.7620
  time to fit residues: 21.0485
Evaluate side-chains
  26 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain FF residue   35 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.118270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.082780 restraints weight = 3359.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 3.04
r_work: 0.3201 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3060  Z= 0.214
  Angle     :  0.536   6.086   4116  Z= 0.294
  Chirality :  0.058   0.126    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.165  19.937    432
  Min Nonbonded Distance : 2.680

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 32.64 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.61 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR D  10 
 PHE   0.012   0.003   PHE C  19 
 HIS   0.006   0.003   HISCC  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 3048)
  covalent geometry    : angle       0.53815 ( 4080)
  hydrogen bonds       : bond        0.03092 (   80)
  hydrogen bonds       : angle       4.67929 (  240)
  link_TRANS           : bond        0.00065 (   12)
  link_TRANS           : angle       0.20074 (   36)

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

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

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  696 Ramachandran restraints generated.
    348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.113 
Fit side-chains
REVERT: D   17 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8162 (tt)
REVERT: D   28 LYS cc_start: 0.8221 (mtpm) cc_final: 0.7729 (mttp)
REVERT: C   28 LYS cc_start: 0.8275 (mtpm) cc_final: 0.7821 (mttp)
REVERT: B   28 LYS cc_start: 0.8372 (mtpm) cc_final: 0.7817 (mttp)
REVERT: A   28 LYS cc_start: 0.8760 (mtpm) cc_final: 0.8355 (mttp)
REVERT: FF   35 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7554 (ttm)
REVERT: DD   28 LYS cc_start: 0.8154 (mtpm) cc_final: 0.7652 (mttp)
REVERT: CC   28 LYS cc_start: 0.8131 (mtpm) cc_final: 0.7685 (mttp)
REVERT: BB   28 LYS cc_start: 0.8291 (mtpm) cc_final: 0.7705 (mttp)
REVERT: AA   28 LYS cc_start: 0.8668 (mtpm) cc_final: 0.8075 (mttp)
  outliers start: 5
  outliers final: 2
  residues processed: 28
  average time/residue: 0.7720
  time to fit residues: 22.0803
Evaluate side-chains
  28 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain CC residue   39 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0170
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.0622

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.116479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.080474 restraints weight = 3371.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.03
r_work: 0.3203 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   3060  Z= 0.200
  Angle     :  0.527   6.086   4116  Z= 0.288
  Chirality :  0.058   0.125    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.152  20.286    432
  Min Nonbonded Distance : 2.680

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 31.25 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.56 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR D  10 
 PHE   0.011   0.002   PHE A  20 
 HIS   0.006   0.002   HISDD  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 3048)
  covalent geometry    : angle       0.52857 ( 4080)
  hydrogen bonds       : bond        0.03019 (   80)
  hydrogen bonds       : angle       4.66942 (  240)
  link_TRANS           : bond        0.00060 (   12)
  link_TRANS           : angle       0.22725 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1149.85 seconds
wall clock time: 20 minutes 18.41 seconds (1218.41 seconds total)