Starting phenix.real_space_refine
on Wed Jun  4 17:12:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9byn_45039/06_2025/9byn_45039.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9byn_45039/06_2025/9byn_45039.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9byn_45039/06_2025/9byn_45039.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9byn_45039/06_2025/9byn_45039.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9byn_45039/06_2025/9byn_45039.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9byn_45039/06_2025/9byn_45039.cif"
  }
  resolution = 3.36
  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=   0.005
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      10      5.16       5
     C    2300      2.51       5
     N     585      2.21       5
     O     665      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3560
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 712
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.27, per 1000 atoms: 0.64
  Number of scatterers: 3560
  At special positions: 0
  Unit cell: (92.708, 70.004, 41.624, 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      10     16.00
     O     665      8.00
     N     585      7.00
     C    2300      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
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 449.9 milliseconds
  

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  860

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 39.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16
      removed outlier: 6.376A  pdb=" N   VAL A  14 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   VAL C  14 " --> pdb=" O   LYS E  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 21
      removed outlier: 6.454A  pdb=" N   ALA B  19 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ALA A  19 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 27
      removed outlier: 6.683A  pdb=" N   ALA B  25 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ALA A  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 30 through 32
      removed outlier: 6.526A  pdb=" N   HIS B  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   HIS A  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 62
      removed outlier: 6.571A  pdb=" N   THR B  60 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   THR A  60 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 68
      removed outlier: 7.064A  pdb=" N   ILE D  68 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ILE B  68 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   GLU A  66 " --> pdb=" O   GLY C  67 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   GLU C  66 " --> pdb=" O   GLY E  67 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 73
      removed outlier: 6.556A  pdb=" N   GLU A  72 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLU C  72 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 78 through 80
      removed outlier: 8.027A  pdb=" N   TYR B  78 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   TYR A  78 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   LYS C  80 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LYS E  80 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 99
      removed outlier: 6.561A  pdb=" N   VAL B  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   THR D  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   PHE B  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ASN D  98 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   ALA B  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL A  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   THR B  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   PHE A  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ASN B  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   ALA A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 103 through 108
      removed outlier: 6.827A  pdb=" N   ARG A 104 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   ILE C 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   THR A 106 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ARG C 104 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   ILE E 107 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   THR C 106 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 115
      removed outlier: 7.017A  pdb=" N   TYR A 114 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   TYR C 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 118 through 122
      removed outlier: 5.922A  pdb=" N   THR B 118 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   VAL D 121 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ALA B 120 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   THR A 118 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   VAL B 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ALA A 120 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)

    68 hydrogen bonds defined for protein.
    204 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: 0.92

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1110
        1.34 -     1.45: 516
        1.45 -     1.57: 1994
        1.57 -     1.69: 0
        1.69 -     1.80: 20
  Bond restraints: 3640
  Sorted by residual:
  bond pdb=" CG1 ILE E 107 "
       pdb=" CD1 ILE E 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.480  0.033 3.90e-02 6.57e+02 7.18e-01
  bond pdb=" CG1 ILE D 107 "
       pdb=" CD1 ILE D 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.90e-01
  bond pdb=" CG1 ILE C 107 "
       pdb=" CD1 ILE C 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.85e-01
  bond pdb=" CG1 ILE A 107 "
       pdb=" CD1 ILE A 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.78e-01
  bond pdb=" CG1 ILE B 107 "
       pdb=" CD1 ILE B 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.68e-01
  ... (remaining 3635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 4576
        1.06 -     2.12: 278
        2.12 -     3.18: 61
        3.18 -     4.24: 25
        4.24 -     5.30: 5
  Bond angle restraints: 4945
  Sorted by residual:
  angle pdb=" N   SER C  23 "
        pdb=" CA  SER C  23 "
        pdb=" C   SER C  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.11   -5.30 2.21e+00 2.05e-01 5.76e+00
  angle pdb=" N   SER A  23 "
        pdb=" CA  SER A  23 "
        pdb=" C   SER A  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.09   -5.28 2.21e+00 2.05e-01 5.71e+00
  angle pdb=" N   SER E  23 "
        pdb=" CA  SER E  23 "
        pdb=" C   SER E  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.08   -5.27 2.21e+00 2.05e-01 5.69e+00
  angle pdb=" N   SER B  23 "
        pdb=" CA  SER B  23 "
        pdb=" C   SER B  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.08   -5.27 2.21e+00 2.05e-01 5.69e+00
  angle pdb=" N   SER D  23 "
        pdb=" CA  SER D  23 "
        pdb=" C   SER D  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.08   -5.27 2.21e+00 2.05e-01 5.68e+00
  ... (remaining 4940 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.16: 1780
       10.16 -    20.32: 222
       20.32 -    30.48: 98
       30.48 -    40.64: 20
       40.64 -    50.80: 25
  Dihedral angle restraints: 2145
    sinusoidal: 815
      harmonic: 1330
  Sorted by residual:
  dihedral pdb=" CA  GLY D  67 "
           pdb=" C   GLY D  67 "
           pdb=" N   ILE D  68 "
           pdb=" CA  ILE D  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.03   15.97     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  GLY E  67 "
           pdb=" C   GLY E  67 "
           pdb=" N   ILE E  68 "
           pdb=" CA  ILE E  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.03   15.97     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  GLY A  67 "
           pdb=" C   GLY A  67 "
           pdb=" N   ILE A  68 "
           pdb=" CA  ILE A  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.03   15.97     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 2142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 242
       0.025 -    0.050: 168
       0.050 -    0.075: 66
       0.075 -    0.100: 50
       0.100 -    0.125: 54
  Chirality restraints: 580
  Sorted by residual:
  chirality pdb=" CA  SER E  85 "
            pdb=" N   SER E  85 "
            pdb=" C   SER E  85 "
            pdb=" CB  SER E  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.89e-01
  chirality pdb=" CA  SER A  85 "
            pdb=" N   SER A  85 "
            pdb=" C   SER A  85 "
            pdb=" CB  SER A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  SER D  85 "
            pdb=" N   SER D  85 "
            pdb=" C   SER D  85 "
            pdb=" CB  SER D  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 577 not shown)

  Planarity restraints: 610
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 100 "   -0.006 2.00e-02 2.50e+03   1.26e-02 1.58e+00
        pdb=" C   SER C 100 "    0.022 2.00e-02 2.50e+03
        pdb=" O   SER C 100 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLY C 101 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E 100 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.57e+00
        pdb=" C   SER E 100 "    0.022 2.00e-02 2.50e+03
        pdb=" O   SER E 100 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLY E 101 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 100 "   -0.006 2.00e-02 2.50e+03   1.24e-02 1.54e+00
        pdb=" C   SER D 100 "    0.021 2.00e-02 2.50e+03
        pdb=" O   SER D 100 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLY D 101 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 607 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 151
        2.72 -     3.27: 3132
        3.27 -     3.81: 5694
        3.81 -     4.36: 6366
        4.36 -     4.90: 11140
  Nonbonded interactions: 26483
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 112 "
            pdb=" O   SER B 112 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" O   SER A 112 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   SER D  85 "
            pdb=" OG  SER D  85 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O   SER E  85 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O   SER A  85 "
            pdb=" OG  SER A  85 "
     model   vdw
     2.190 3.040
  ... (remaining 26478 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 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.200
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.300
  Find NCS groups from input model:        0.080
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
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      :  0.006   0.033   3640  Z= 0.248
  Angle     :  0.659   5.303   4945  Z= 0.357
  Chirality :  0.052   0.125    580
  Planarity :  0.005   0.027    610
  Dihedral  : 12.739  50.799   1285
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.58 %
    Favored  : 84.42 %
  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: -2.21 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP E  79 
 HIS   0.002   0.001   HIS E  90 
 PHE   0.014   0.003   PHE B  33 
 TYR   0.017   0.003   TYR D  78 
 ARG   0.003   0.001   ARG C 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25280 (   68)
  hydrogen bonds       : angle       8.32210 (  204)
  covalent geometry    : bond        0.00563 ( 3640)
  covalent geometry    : angle       0.65912 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.422 
Fit side-chains
REVERT: B   35 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7428 (mttt)
REVERT: D   35 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7473 (tttt)
REVERT: D   80 LYS cc_start: 0.8776 (tttt) cc_final: 0.8567 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2072
  time to fit residues: 12.5029
Evaluate side-chains
  49 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.117556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.088728 restraints weight = 3937.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.84
r_work: 0.3305 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.0991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3640  Z= 0.180
  Angle     :  0.607   5.562   4945  Z= 0.328
  Chirality :  0.049   0.171    580
  Planarity :  0.004   0.035    610
  Dihedral  :  5.386  16.198    490
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 11.95 %
    Favored  : 85.45 %
  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: -2.29 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.002   0.001   HIS C  31 
 PHE   0.010   0.002   PHE D  33 
 TYR   0.021   0.002   TYR C  78 
 ARG   0.001   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04816 (   68)
  hydrogen bonds       : angle       5.84629 (  204)
  covalent geometry    : bond        0.00423 ( 3640)
  covalent geometry    : angle       0.60738 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7522 (mtt-85)
REVERT: C  104 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7688 (mtt-85)
REVERT: D   35 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7554 (mttt)
REVERT: D   62 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7538 (tt0)
REVERT: D   80 LYS cc_start: 0.8425 (tttt) cc_final: 0.8217 (tttm)
REVERT: E   92 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7346 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 55
  average time/residue: 0.2473
  time to fit residues: 15.8613
Evaluate side-chains
  57 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    0.0970
   chunk 22 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.117360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.087809 restraints weight = 3869.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.89
r_work: 0.3277 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3640  Z= 0.181
  Angle     :  0.610   5.455   4945  Z= 0.328
  Chirality :  0.051   0.182    580
  Planarity :  0.003   0.036    610
  Dihedral  :  5.386  16.545    490
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.03 %
    Favored  : 83.12 %
  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: -2.31 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  79 
 HIS   0.002   0.000   HIS A  31 
 PHE   0.011   0.002   PHE E  95 
 TYR   0.021   0.003   TYR A  78 
 ARG   0.001   0.000   ARG E  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04445 (   68)
  hydrogen bonds       : angle       5.50112 (  204)
  covalent geometry    : bond        0.00436 ( 3640)
  covalent geometry    : angle       0.60992 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7425 (tt0) cc_final: 0.6881 (tt0)
REVERT: A  104 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7443 (mtt-85)
REVERT: C  104 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7693 (mtt-85)
REVERT: D   35 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7500 (mttt)
REVERT: D   62 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7487 (tt0)
REVERT: D   80 LYS cc_start: 0.8342 (tttt) cc_final: 0.8117 (tttm)
REVERT: E   92 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7413 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 53
  average time/residue: 0.2309
  time to fit residues: 14.3005
Evaluate side-chains
  59 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   61 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0170
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.8024

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

Flipped N/Q/H residues before XYZ refinement:
B  31 HIS
D  31 HIS
E  31 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.114273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.085491 restraints weight = 3986.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.85
r_work: 0.3248 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3640  Z= 0.221
  Angle     :  0.627   5.415   4945  Z= 0.340
  Chirality :  0.051   0.168    580
  Planarity :  0.003   0.031    610
  Dihedral  :  5.530  16.813    490
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.51 %
    Favored  : 83.64 %
  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: -2.41 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  79 
 HIS   0.001   0.000   HIS C  31 
 PHE   0.013   0.002   PHE E  95 
 TYR   0.023   0.003   TYR C  78 
 ARG   0.002   0.000   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04338 (   68)
  hydrogen bonds       : angle       5.34327 (  204)
  covalent geometry    : bond        0.00534 ( 3640)
  covalent geometry    : angle       0.62741 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7369 (tt0) cc_final: 0.6856 (tt0)
REVERT: A  104 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7640 (mtt-85)
REVERT: B   61 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7215 (mp0)
REVERT: C  104 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7917 (mtt-85)
REVERT: D   61 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7222 (pm20)
REVERT: D   80 LYS cc_start: 0.8393 (tttt) cc_final: 0.8167 (tttm)
REVERT: E   92 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7473 (tm-30)
REVERT: E  104 ARG cc_start: 0.8231 (mtt180) cc_final: 0.7950 (mtt-85)
  outliers start: 11
  outliers final: 8
  residues processed: 53
  average time/residue: 0.2552
  time to fit residues: 15.6769
Evaluate side-chains
  61 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0070
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.7598

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.122691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.093642 restraints weight = 4014.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.74
r_work: 0.3360 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3640  Z= 0.119
  Angle     :  0.549   5.200   4945  Z= 0.294
  Chirality :  0.049   0.160    580
  Planarity :  0.003   0.031    610
  Dihedral  :  5.235  14.948    490
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 14.55 %
    Favored  : 83.12 %
  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: -2.35 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A  79 
 HIS   0.003   0.000   HIS A  31 
 PHE   0.007   0.001   PHE E  95 
 TYR   0.014   0.002   TYR C  78 
 ARG   0.002   0.000   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02995 (   68)
  hydrogen bonds       : angle       5.13416 (  204)
  covalent geometry    : bond        0.00282 ( 3640)
  covalent geometry    : angle       0.54872 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7593 (tt0) cc_final: 0.7113 (tt0)
REVERT: A  104 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7781 (mtt-85)
REVERT: C   30 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7520 (tpp)
REVERT: D   35 LYS cc_start: 0.8123 (mttt) cc_final: 0.7872 (mmmt)
REVERT: D   80 LYS cc_start: 0.8569 (tttt) cc_final: 0.8353 (tttm)
REVERT: E   92 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7598 (tm-30)
REVERT: E  104 ARG cc_start: 0.8371 (mtt180) cc_final: 0.8066 (mtt-85)
  outliers start: 9
  outliers final: 5
  residues processed: 54
  average time/residue: 0.2522
  time to fit residues: 15.8246
Evaluate side-chains
  57 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   61 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0270
   chunk 10 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    2.3244

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

Flipped N/Q/H residues before XYZ refinement:
A  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.114301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.084748 restraints weight = 3996.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.87
r_work: 0.3261 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035   3640  Z= 0.273
  Angle     :  0.656   5.647   4945  Z= 0.358
  Chirality :  0.053   0.175    580
  Planarity :  0.004   0.027    610
  Dihedral  :  5.603  17.074    490
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.55 %
    Favored  : 82.08 %
  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: -2.59 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  79 
 HIS   0.004   0.001   HIS E  31 
 PHE   0.015   0.003   PHE E  95 
 TYR   0.024   0.003   TYR C  78 
 ARG   0.002   0.000   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04709 (   68)
  hydrogen bonds       : angle       5.20890 (  204)
  covalent geometry    : bond        0.00658 ( 3640)
  covalent geometry    : angle       0.65644 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7450 (tt0) cc_final: 0.6942 (tt0)
REVERT: A  104 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7661 (mtt-85)
REVERT: B   61 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7229 (mp0)
REVERT: D   35 LYS cc_start: 0.8115 (mttt) cc_final: 0.7820 (mmmt)
REVERT: D   80 LYS cc_start: 0.8464 (tttt) cc_final: 0.8240 (tttm)
REVERT: E   92 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7503 (tm-30)
REVERT: E  104 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7981 (mtt-85)
  outliers start: 13
  outliers final: 10
  residues processed: 56
  average time/residue: 0.2445
  time to fit residues: 15.9515
Evaluate side-chains
  65 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 31 optimal weight:    0.3980
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   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 = 0.3931 r_free = 0.3931 target = 0.121273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.093692 restraints weight = 3878.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.65
r_work: 0.3370 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3640  Z= 0.109
  Angle     :  0.544   5.232   4945  Z= 0.291
  Chirality :  0.050   0.165    580
  Planarity :  0.003   0.027    610
  Dihedral  :  5.189  15.307    490
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 17.92 %
    Favored  : 80.78 %
  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: -2.40 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B  79 
 HIS   0.003   0.000   HIS C  31 
 PHE   0.006   0.001   PHE E  95 
 TYR   0.014   0.002   TYR B 114 
 ARG   0.001   0.000   ARG C 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02688 (   68)
  hydrogen bonds       : angle       4.95709 (  204)
  covalent geometry    : bond        0.00260 ( 3640)
  covalent geometry    : angle       0.54382 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7528 (tt0) cc_final: 0.7024 (tt0)
REVERT: A  104 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7635 (mtt-85)
REVERT: C   30 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7545 (tpp)
REVERT: D   35 LYS cc_start: 0.8172 (mttt) cc_final: 0.7905 (mmmt)
REVERT: D   80 LYS cc_start: 0.8529 (tttt) cc_final: 0.8306 (tttm)
REVERT: E   92 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7542 (tm-30)
REVERT: E  104 ARG cc_start: 0.8332 (mtt180) cc_final: 0.8020 (mtt-85)
  outliers start: 5
  outliers final: 3
  residues processed: 54
  average time/residue: 0.2522
  time to fit residues: 15.7715
Evaluate side-chains
  56 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3832 r_free = 0.3832 target = 0.113853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.084474 restraints weight = 3931.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.82
r_work: 0.3251 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   3640  Z= 0.274
  Angle     :  0.660   5.725   4945  Z= 0.361
  Chirality :  0.053   0.172    580
  Planarity :  0.004   0.024    610
  Dihedral  :  5.625  17.123    490
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.57 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.10 %
    Favored  : 80.78 %
  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: -2.64 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.004   0.001   HIS B  31 
 PHE   0.016   0.003   PHE A  95 
 TYR   0.023   0.003   TYR C  78 
 ARG   0.003   0.001   ARG C  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04663 (   68)
  hydrogen bonds       : angle       5.14943 (  204)
  covalent geometry    : bond        0.00659 ( 3640)
  covalent geometry    : angle       0.66043 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7435 (tt0) cc_final: 0.6925 (tt0)
REVERT: A  104 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7630 (mtt-85)
REVERT: D   35 LYS cc_start: 0.8156 (mttt) cc_final: 0.7854 (mmmt)
REVERT: D   80 LYS cc_start: 0.8439 (tttt) cc_final: 0.8210 (tttp)
REVERT: E   92 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7526 (tm-30)
REVERT: E  104 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7993 (mtt-85)
  outliers start: 12
  outliers final: 10
  residues processed: 55
  average time/residue: 0.2907
  time to fit residues: 18.2327
Evaluate side-chains
  63 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.114769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.086272 restraints weight = 3865.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.76
r_work: 0.3335 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3640  Z= 0.194
  Angle     :  0.603   5.529   4945  Z= 0.327
  Chirality :  0.051   0.170    580
  Planarity :  0.003   0.027    610
  Dihedral  :  5.528  16.629    490
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.18 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.64 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  79 
 HIS   0.002   0.001   HIS E  31 
 PHE   0.011   0.002   PHE E  95 
 TYR   0.020   0.002   TYR C  78 
 ARG   0.002   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03832 (   68)
  hydrogen bonds       : angle       5.04255 (  204)
  covalent geometry    : bond        0.00468 ( 3640)
  covalent geometry    : angle       0.60335 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7460 (tt0) cc_final: 0.6947 (tt0)
REVERT: A  104 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7649 (mtt-85)
REVERT: D   35 LYS cc_start: 0.8128 (mttt) cc_final: 0.7869 (mmmt)
REVERT: D   80 LYS cc_start: 0.8528 (tttt) cc_final: 0.8319 (tttp)
REVERT: E   92 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7490 (tm-30)
REVERT: E  104 ARG cc_start: 0.8267 (mtt180) cc_final: 0.8024 (mtt-85)
  outliers start: 7
  outliers final: 7
  residues processed: 53
  average time/residue: 0.2662
  time to fit residues: 16.2446
Evaluate side-chains
  59 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   61 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.117463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.088253 restraints weight = 3905.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.81
r_work: 0.3311 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3640  Z= 0.166
  Angle     :  0.582   5.495   4945  Z= 0.315
  Chirality :  0.050   0.167    580
  Planarity :  0.003   0.025    610
  Dihedral  :  5.374  16.170    490
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 18.18 %
    Favored  : 80.26 %
  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: -2.56 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B  79 
 HIS   0.002   0.001   HIS E  31 
 PHE   0.010   0.002   PHE E  95 
 TYR   0.018   0.002   TYR C  78 
 ARG   0.001   0.000   ARG C  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (   68)
  hydrogen bonds       : angle       4.98961 (  204)
  covalent geometry    : bond        0.00403 ( 3640)
  covalent geometry    : angle       0.58156 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7431 (tt0) cc_final: 0.6919 (tt0)
REVERT: A  104 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7567 (mtt-85)
REVERT: D   35 LYS cc_start: 0.8051 (mttt) cc_final: 0.7801 (mmmt)
REVERT: D   80 LYS cc_start: 0.8441 (tttt) cc_final: 0.8220 (tttm)
REVERT: E   13 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6525 (tmm)
REVERT: E   92 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7486 (tm-30)
REVERT: E  104 ARG cc_start: 0.8246 (mtt180) cc_final: 0.7936 (mtt-85)
  outliers start: 6
  outliers final: 4
  residues processed: 52
  average time/residue: 0.2507
  time to fit residues: 15.0876
Evaluate side-chains
  56 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   61 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0970
   chunk 20 optimal weight:    9.9990
   chunk 37 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0570
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.4496

-------------------------------------------------------------------------------
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 = 0.3940 r_free = 0.3940 target = 0.121162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.092313 restraints weight = 3837.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.79
r_work: 0.3371 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3640  Z= 0.098
  Angle     :  0.532   5.189   4945  Z= 0.285
  Chirality :  0.049   0.161    580
  Planarity :  0.003   0.028    610
  Dihedral  :  5.085  15.518    490
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 18.44 %
    Favored  : 80.52 %
  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: -2.39 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP C  79 
 HIS   0.002   0.000   HIS C  31 
 PHE   0.005   0.001   PHE E  95 
 TYR   0.013   0.001   TYR B 114 
 ARG   0.001   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02551 (   68)
  hydrogen bonds       : angle       4.82132 (  204)
  covalent geometry    : bond        0.00234 ( 3640)
  covalent geometry    : angle       0.53178 ( 4945)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2198.24 seconds
wall clock time: 38 minutes 25.98 seconds (2305.98 seconds total)