Starting phenix.real_space_refine
on Sat Apr 26 18:14:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jaz_61302/04_2025/9jaz_61302.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jaz_61302/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jaz_61302/04_2025/9jaz_61302.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jaz_61302/04_2025/9jaz_61302.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jaz_61302/04_2025/9jaz_61302.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jaz_61302/04_2025/9jaz_61302.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3012
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 121
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
    Chain: "A"
      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:
    AA, C, B, E, D, BB, F, EE, DD, CC, FF
  Time building chain proxies: 1.37, per 1000 atoms: 0.45
  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: 0.73
  Conformation dependent library (CDL) restraints added in 341.5 milliseconds
  

  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: 0.59
  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: 0.74

  Time building geometry restraints manager: 0.87 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'AA'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'BB'
  selection = chain 'F'
  selection = chain 'EE'
  selection = chain 'DD'
  selection = chain 'CC'
  selection = chain 'FF'
}

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:             1.020
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.190
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.003   0.002   HIS C  13 
 PHE   0.007   0.002   PHE B  20 
 TYR   0.003   0.001   TYR C  10 

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

*********************** 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  : 0.337 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8573 (mtpm) cc_final: 0.8161 (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: 0.8019 (mttp)
REVERT: A   28 LYS cc_start: 0.8891 (mtpm) cc_final: 0.8508 (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: 0.8104 (mttp)
REVERT: BB   28 LYS cc_start: 0.8374 (mtpm) cc_final: 0.7866 (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: 2.0868
  time to fit residues: 51.2831
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  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.0182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.115745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.080456 restraints weight = 3357.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.95
r_work: 0.3212 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.0819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3060  Z= 0.196
  Angle     :  0.496   4.959   4116  Z= 0.279
  Chirality :  0.058   0.129    468
  Planarity :  0.002   0.007    516
  Dihedral  :  4.937  14.522    432
  Min Nonbonded Distance : 2.694

Molprobity Statistics.
  All-atom Clashscore : 4.98
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.45), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.57 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS D  13 
 PHE   0.011   0.002   PHE A  20 
 TYR   0.003   0.001   TYR F  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00083 (   12)
  link_TRANS           : angle       0.18810 (   36)
  hydrogen bonds       : bond        0.03873 (   80)
  hydrogen bonds       : angle       5.02794 (  240)
  covalent geometry    : bond        0.00477 ( 3048)
  covalent geometry    : angle       0.49826 ( 4080)

*********************** 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  : 0.287 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8136 (mtpm) cc_final: 0.7680 (mttp)
REVERT: C   28 LYS cc_start: 0.8177 (mtpm) cc_final: 0.7677 (mttp)
REVERT: B   28 LYS cc_start: 0.8277 (mtpm) cc_final: 0.7721 (mttp)
REVERT: A   28 LYS cc_start: 0.8684 (mtpm) cc_final: 0.8245 (mttm)
REVERT: DD   28 LYS cc_start: 0.8081 (mtpm) cc_final: 0.7592 (mttm)
REVERT: CC   28 LYS cc_start: 0.8104 (mtpm) cc_final: 0.7669 (mttp)
REVERT: CC   35 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8113 (ttt)
REVERT: BB   28 LYS cc_start: 0.8119 (mtpm) cc_final: 0.7551 (mttp)
REVERT: AA   28 LYS cc_start: 0.8607 (mtpm) cc_final: 0.7981 (mttp)
  outliers start: 5
  outliers final: 3
  residues processed: 24
  average time/residue: 2.0192
  time to fit residues: 49.6010
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  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain DD residue   35 MET
Chi-restraints excluded: chain CC residue   35 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    0.3980
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3889 r_free = 0.3889 target = 0.116873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.081285 restraints weight = 3377.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.99
r_work: 0.3163 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1099

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= 0.200
  Angle     :  0.488   5.147   4116  Z= 0.277
  Chirality :  0.058   0.127    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.148  15.891    432
  Min Nonbonded Distance : 2.692

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 30.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (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
 HIS   0.005   0.002   HISDD  13 
 PHE   0.011   0.002   PHE A  20 
 TYR   0.004   0.001   TYR E  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00088 (   12)
  link_TRANS           : angle       0.15469 (   36)
  hydrogen bonds       : bond        0.03321 (   80)
  hydrogen bonds       : angle       4.79227 (  240)
  covalent geometry    : bond        0.00479 ( 3048)
  covalent geometry    : angle       0.49000 ( 4080)

*********************** 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  : 0.302 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8255 (mtpm) cc_final: 0.7797 (mttp)
REVERT: C   28 LYS cc_start: 0.8300 (mtpm) cc_final: 0.7792 (mttp)
REVERT: B   28 LYS cc_start: 0.8405 (mtpm) cc_final: 0.7881 (mttp)
REVERT: A   28 LYS cc_start: 0.8782 (mtpm) cc_final: 0.8362 (mttp)
REVERT: FF   35 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7643 (ttm)
REVERT: DD   28 LYS cc_start: 0.8192 (mtpm) cc_final: 0.7727 (mttp)
REVERT: CC   28 LYS cc_start: 0.8196 (mtpm) cc_final: 0.7771 (mttp)
REVERT: BB   28 LYS cc_start: 0.8280 (mtpm) cc_final: 0.7708 (mttp)
REVERT: AA   28 LYS cc_start: 0.8674 (mtpm) cc_final: 0.8059 (mttp)
  outliers start: 12
  outliers final: 4
  residues processed: 30
  average time/residue: 1.7030
  time to fit residues: 52.4351
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  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 MET
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.118461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.081496 restraints weight = 3404.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 3.11
r_work: 0.3184 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1268

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= 0.170
  Angle     :  0.467   5.286   4116  Z= 0.264
  Chirality :  0.057   0.124    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.089  16.063    432
  Min Nonbonded Distance : 2.692

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 29.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.64 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HISDD  13 
 PHE   0.010   0.002   PHE A  20 
 TYR   0.003   0.001   TYRDD  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00058 (   12)
  link_TRANS           : angle       0.15366 (   36)
  hydrogen bonds       : bond        0.02965 (   80)
  hydrogen bonds       : angle       4.69875 (  240)
  covalent geometry    : bond        0.00407 ( 3048)
  covalent geometry    : angle       0.46883 ( 4080)

*********************** 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
  36 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 0.321 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8237 (mtpm) cc_final: 0.7766 (mttp)
REVERT: C   28 LYS cc_start: 0.8245 (mtpm) cc_final: 0.7733 (mttp)
REVERT: B   28 LYS cc_start: 0.8376 (mtpm) cc_final: 0.7836 (mttp)
REVERT: A   28 LYS cc_start: 0.8757 (mtpm) cc_final: 0.8350 (mttp)
REVERT: FF   35 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7614 (ttm)
REVERT: DD   28 LYS cc_start: 0.8178 (mtpm) cc_final: 0.7701 (mttp)
REVERT: CC   28 LYS cc_start: 0.8148 (mtpm) cc_final: 0.7720 (mttp)
REVERT: BB   28 LYS cc_start: 0.8281 (mtpm) cc_final: 0.7717 (mttp)
REVERT: AA   28 LYS cc_start: 0.8631 (mtpm) cc_final: 0.8014 (mttp)
  outliers start: 12
  outliers final: 3
  residues processed: 29
  average time/residue: 1.6066
  time to fit residues: 47.8483
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  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3896 r_free = 0.3896 target = 0.116648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.080439 restraints weight = 3448.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 3.06
r_work: 0.3171 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3060  Z= 0.218
  Angle     :  0.513   5.400   4116  Z= 0.288
  Chirality :  0.058   0.127    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.152  17.361    432
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 29.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.45), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.57 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HISDD  13 
 PHE   0.012   0.003   PHE A  20 
 TYR   0.004   0.001   TYR E  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00096 (   12)
  link_TRANS           : angle       0.15051 (   36)
  hydrogen bonds       : bond        0.03138 (   80)
  hydrogen bonds       : angle       4.71060 (  240)
  covalent geometry    : bond        0.00520 ( 3048)
  covalent geometry    : angle       0.51502 ( 4080)

*********************** 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
  39 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 24
  time to evaluate  : 0.285 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8217 (mtpm) cc_final: 0.7731 (mttp)
REVERT: C   28 LYS cc_start: 0.8213 (mtpm) cc_final: 0.7712 (mttp)
REVERT: B   28 LYS cc_start: 0.8333 (mtpm) cc_final: 0.7807 (mttp)
REVERT: A   28 LYS cc_start: 0.8719 (mtpm) cc_final: 0.8308 (mttp)
REVERT: FF   35 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7579 (ttm)
REVERT: DD   28 LYS cc_start: 0.8157 (mtpm) cc_final: 0.7699 (mttp)
REVERT: CC   28 LYS cc_start: 0.8124 (mtpm) cc_final: 0.7686 (mttp)
REVERT: BB   28 LYS cc_start: 0.8262 (mtpm) cc_final: 0.7679 (mttp)
REVERT: AA   28 LYS cc_start: 0.8596 (mtpm) cc_final: 0.7980 (mttp)
REVERT: AA   35 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8233 (tpp)
  outliers start: 15
  outliers final: 1
  residues processed: 30
  average time/residue: 1.5263
  time to fit residues: 47.0100
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  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain DD residue   35 MET
Chi-restraints excluded: chain AA residue   35 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.8988

-------------------------------------------------------------------------------
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 = 0.3840 r_free = 0.3840 target = 0.113238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.077623 restraints weight = 3455.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.05
r_work: 0.3133 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.039   3060  Z= 0.332
  Angle     :  0.615   5.618   4116  Z= 0.342
  Chirality :  0.060   0.132    468
  Planarity :  0.003   0.008    516
  Dihedral  :  5.531  21.254    432
  Min Nonbonded Distance : 2.680

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 28.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (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
 HIS   0.007   0.003   HISDD  13 
 PHE   0.016   0.003   PHE C  19 
 TYR   0.006   0.001   TYR E  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00188 (   12)
  link_TRANS           : angle       0.17018 (   36)
  hydrogen bonds       : bond        0.03384 (   80)
  hydrogen bonds       : angle       4.69241 (  240)
  covalent geometry    : bond        0.00794 ( 3048)
  covalent geometry    : angle       0.61757 ( 4080)

*********************** 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  : 0.315 
Fit side-chains
REVERT: D   17 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8121 (tt)
REVERT: D   28 LYS cc_start: 0.8233 (mtpm) cc_final: 0.7754 (mttp)
REVERT: C   28 LYS cc_start: 0.8238 (mtpm) cc_final: 0.7737 (mttp)
REVERT: B   28 LYS cc_start: 0.8403 (mtpm) cc_final: 0.7856 (mttp)
REVERT: A   28 LYS cc_start: 0.8785 (mtpm) cc_final: 0.8342 (mttm)
REVERT: FF   35 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7531 (ttm)
REVERT: DD   28 LYS cc_start: 0.8182 (mtpm) cc_final: 0.7718 (mttp)
REVERT: CC   17 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8135 (tt)
REVERT: CC   28 LYS cc_start: 0.8171 (mtpm) cc_final: 0.7738 (mttp)
REVERT: BB   28 LYS cc_start: 0.8290 (mtpm) cc_final: 0.7706 (mttp)
REVERT: AA   28 LYS cc_start: 0.8676 (mtpm) cc_final: 0.8107 (mttp)
REVERT: AA   35 MET cc_start: 0.8929 (ttp) cc_final: 0.8636 (tpp)
  outliers start: 14
  outliers final: 4
  residues processed: 31
  average time/residue: 1.4985
  time to fit residues: 47.7492
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  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain DD residue   35 MET
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 27 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0010
   chunk 24 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0030
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0030
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.3006

-------------------------------------------------------------------------------
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 = 0.3960 r_free = 0.3960 target = 0.121429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.085605 restraints weight = 3255.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.98
r_work: 0.3288 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3060  Z= 0.090
  Angle     :  0.434   5.640   4116  Z= 0.242
  Chirality :  0.057   0.127    468
  Planarity :  0.001   0.007    516
  Dihedral  :  4.856  19.123    432
  Min Nonbonded Distance : 2.692

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 30.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (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
 HIS   0.003   0.001   HISDD  13 
 PHE   0.005   0.001   PHE D  20 
 TYR   0.003   0.001   TYRDD  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00030 (   12)
  link_TRANS           : angle       0.34377 (   36)
  hydrogen bonds       : bond        0.02617 (   80)
  hydrogen bonds       : angle       4.66456 (  240)
  covalent geometry    : bond        0.00205 ( 3048)
  covalent geometry    : angle       0.43478 ( 4080)

*********************** 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
  32 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.261 
Fit side-chains
REVERT: D   28 LYS cc_start: 0.8161 (mtpm) cc_final: 0.7688 (mttp)
REVERT: C   28 LYS cc_start: 0.8161 (mtpm) cc_final: 0.7657 (mttp)
REVERT: B   28 LYS cc_start: 0.8273 (mtpm) cc_final: 0.7726 (mttp)
REVERT: A   28 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8195 (mttp)
REVERT: FF   35 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7214 (ttm)
REVERT: DD   28 LYS cc_start: 0.8097 (mtpm) cc_final: 0.7581 (mttp)
REVERT: CC   28 LYS cc_start: 0.8037 (mtpm) cc_final: 0.7581 (mttp)
REVERT: BB   28 LYS cc_start: 0.8207 (mtpm) cc_final: 0.7675 (mtmm)
REVERT: AA   28 LYS cc_start: 0.8574 (mtpm) cc_final: 0.8136 (mttp)
  outliers start: 8
  outliers final: 0
  residues processed: 27
  average time/residue: 1.6590
  time to fit residues: 45.9059
Evaluate side-chains
  25 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain FF residue   35 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0060
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.1600

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.116331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.080644 restraints weight = 3352.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 3.03
r_work: 0.3197 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1716

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= 0.218
  Angle     :  0.530   5.858   4116  Z= 0.292
  Chirality :  0.058   0.126    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.175  20.438    432
  Min Nonbonded Distance : 2.690

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 29.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.57 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HISDD  13 
 PHE   0.012   0.003   PHE C  19 
 TYR   0.004   0.001   TYR E  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00078 (   12)
  link_TRANS           : angle       0.19951 (   36)
  hydrogen bonds       : bond        0.03149 (   80)
  hydrogen bonds       : angle       4.67448 (  240)
  covalent geometry    : bond        0.00523 ( 3048)
  covalent geometry    : angle       0.53191 ( 4080)

*********************** 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
  36 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 0.449 
Fit side-chains
REVERT: D   17 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8065 (tt)
REVERT: D   28 LYS cc_start: 0.8214 (mtpm) cc_final: 0.7739 (mttp)
REVERT: C   28 LYS cc_start: 0.8230 (mtpm) cc_final: 0.7781 (mttp)
REVERT: B   28 LYS cc_start: 0.8342 (mtpm) cc_final: 0.7810 (mttp)
REVERT: A   28 LYS cc_start: 0.8699 (mtpm) cc_final: 0.8313 (mttm)
REVERT: FF   35 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7525 (ttm)
REVERT: DD   28 LYS cc_start: 0.8147 (mtpm) cc_final: 0.7639 (mttp)
REVERT: CC   28 LYS cc_start: 0.8128 (mtpm) cc_final: 0.7692 (mttp)
REVERT: BB   28 LYS cc_start: 0.8253 (mtpm) cc_final: 0.7668 (mttp)
REVERT: AA   28 LYS cc_start: 0.8629 (mtpm) cc_final: 0.8044 (mttp)
  outliers start: 12
  outliers final: 1
  residues processed: 29
  average time/residue: 1.7542
  time to fit residues: 52.2854
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  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain FF residue   35 MET
Chi-restraints excluded: chain CC residue   39 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.118663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.083053 restraints weight = 3303.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 3.00
r_work: 0.3233 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3060  Z= 0.152
  Angle     :  0.480   6.011   4116  Z= 0.266
  Chirality :  0.058   0.123    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.013  19.657    432
  Min Nonbonded Distance : 2.694

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 32.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.44), 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
 HIS   0.005   0.002   HISDD  13 
 PHE   0.009   0.002   PHE A  20 
 TYR   0.004   0.001   TYR D  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00031 (   12)
  link_TRANS           : angle       0.27217 (   36)
  hydrogen bonds       : bond        0.02890 (   80)
  hydrogen bonds       : angle       4.64867 (  240)
  covalent geometry    : bond        0.00367 ( 3048)
  covalent geometry    : angle       0.48146 ( 4080)

*********************** 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
  29 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.283 
Fit side-chains
REVERT: D   17 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8059 (tt)
REVERT: D   28 LYS cc_start: 0.8159 (mtpm) cc_final: 0.7681 (mttp)
REVERT: C   28 LYS cc_start: 0.8164 (mtpm) cc_final: 0.7712 (mttp)
REVERT: B   28 LYS cc_start: 0.8286 (mtpm) cc_final: 0.7733 (mttp)
REVERT: A   28 LYS cc_start: 0.8594 (mtpm) cc_final: 0.8200 (mttp)
REVERT: FF   35 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7215 (ttm)
REVERT: DD   28 LYS cc_start: 0.8080 (mtpm) cc_final: 0.7569 (mttp)
REVERT: CC   28 LYS cc_start: 0.8047 (mtpm) cc_final: 0.7600 (mttp)
REVERT: BB   28 LYS cc_start: 0.8179 (mtpm) cc_final: 0.7583 (mttp)
REVERT: AA   28 LYS cc_start: 0.8570 (mtpm) cc_final: 0.8136 (mttp)
  outliers start: 5
  outliers final: 1
  residues processed: 25
  average time/residue: 1.7488
  time to fit residues: 44.8175
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  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain D 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 23 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 = 0.3854 r_free = 0.3854 target = 0.114302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.078710 restraints weight = 3318.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 3.00
r_work: 0.3157 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   3060  Z= 0.288
  Angle     :  0.582   6.075   4116  Z= 0.322
  Chirality :  0.059   0.129    468
  Planarity :  0.002   0.008    516
  Dihedral  :  5.410  21.514    432
  Min Nonbonded Distance : 2.680

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 30.90 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.007   0.003   HIS D  13 
 PHE   0.015   0.003   PHE C  19 
 TYR   0.005   0.001   TYR E  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00129 (   12)
  link_TRANS           : angle       0.17112 (   36)
  hydrogen bonds       : bond        0.03203 (   80)
  hydrogen bonds       : angle       4.66903 (  240)
  covalent geometry    : bond        0.00689 ( 3048)
  covalent geometry    : angle       0.58430 ( 4080)

********************** 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
  32 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.286 
Fit side-chains
REVERT: D   17 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8066 (tt)
REVERT: D   28 LYS cc_start: 0.8188 (mtpm) cc_final: 0.7688 (mttp)
REVERT: C   28 LYS cc_start: 0.8175 (mtpm) cc_final: 0.7709 (mttp)
REVERT: B   28 LYS cc_start: 0.8318 (mtpm) cc_final: 0.7774 (mttp)
REVERT: A   28 LYS cc_start: 0.8721 (mtpm) cc_final: 0.8295 (mttm)
REVERT: FF   35 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7434 (ttm)
REVERT: DD   28 LYS cc_start: 0.8124 (mtpm) cc_final: 0.7651 (mttp)
REVERT: CC   28 LYS cc_start: 0.8107 (mtpm) cc_final: 0.7677 (mttp)
REVERT: BB   28 LYS cc_start: 0.8248 (mtpm) cc_final: 0.7657 (mttp)
REVERT: AA   28 LYS cc_start: 0.8636 (mtpm) cc_final: 0.8123 (mttp)
REVERT: AA   35 MET cc_start: 0.8824 (ttp) cc_final: 0.8407 (tpp)
  outliers start: 8
  outliers final: 4
  residues processed: 26
  average time/residue: 1.7167
  time to fit residues: 45.7325
Evaluate side-chains
  30 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.117558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.082386 restraints weight = 3293.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.99
r_work: 0.3233 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1846

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= 0.158
  Angle     :  0.493   6.094   4116  Z= 0.272
  Chirality :  0.058   0.124    468
  Planarity :  0.002   0.007    516
  Dihedral  :  5.058  20.670    432
  Min Nonbonded Distance : 2.689

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 30.90 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.44), residues: 348
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.58 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HISDD  13 
 PHE   0.009   0.002   PHE A  20 
 TYR   0.004   0.001   TYR D  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00033 (   12)
  link_TRANS           : angle       0.28418 (   36)
  hydrogen bonds       : bond        0.02897 (   80)
  hydrogen bonds       : angle       4.66026 (  240)
  covalent geometry    : bond        0.00379 ( 3048)
  covalent geometry    : angle       0.49484 ( 4080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2415.76 seconds
wall clock time: 42 minutes 0.02 seconds (2520.02 seconds total)