Starting phenix.real_space_refine
on Tue Feb  3 12:19:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l2s_62779/02_2026/9l2s_62779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l2s_62779/02_2026/9l2s_62779.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l2s_62779/02_2026/9l2s_62779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l2s_62779/02_2026/9l2s_62779.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l2s_62779/02_2026/9l2s_62779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l2s_62779/02_2026/9l2s_62779.map"
  }
  resolution = 3.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C     651      2.51       5
     N     210      2.21       5
     O     258      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1119
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "D"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 81
          Classifications: {'peptide': 13}
          Link IDs: {'TRANS': 12}
    Chain: "G"
      Number of atoms: 123
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 20, 119
          Classifications: {'peptide': 20}
          Link IDs: {'TRANS': 19}
      Conformer: "B"
        Number of residues, atoms: 20, 119
          Classifications: {'peptide': 20}
          Link IDs: {'TRANS': 19}
          bond proxies already assigned to first conformer: 114
    Chain: "A"
      Number of atoms: 169
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 28, 165
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
      Conformer: "B"
        Number of residues, atoms: 28, 165
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
          bond proxies already assigned to first conformer: 160
    Chain: "E"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 81
          Classifications: {'peptide': 13}
          Link IDs: {'TRANS': 12}
    Chain: "H"
      Number of atoms: 123
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 20, 119
          Classifications: {'peptide': 20}
          Link IDs: {'TRANS': 19}
      Conformer: "B"
        Number of residues, atoms: 20, 119
          Classifications: {'peptide': 20}
          Link IDs: {'TRANS': 19}
          bond proxies already assigned to first conformer: 114
    Chain: "B"
      Number of atoms: 169
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 28, 165
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
      Conformer: "B"
        Number of residues, atoms: 28, 165
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
          bond proxies already assigned to first conformer: 160
    Chain: "F"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 81
          Classifications: {'peptide': 13}
          Link IDs: {'TRANS': 12}
    Chain: "I"
      Number of atoms: 123
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 20, 119
          Classifications: {'peptide': 20}
          Link IDs: {'TRANS': 19}
      Conformer: "B"
        Number of residues, atoms: 20, 119
          Classifications: {'peptide': 20}
          Link IDs: {'TRANS': 19}
          bond proxies already assigned to first conformer: 114
    Chain: "C"
      Number of atoms: 169
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 28, 165
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
      Conformer: "B"
        Number of residues, atoms: 28, 165
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
          bond proxies already assigned to first conformer: 160
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  AGLY G  41 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY G  41 " occ=0.50
    residue:
      pdb=" N  AGLY A  41 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A  41 " occ=0.50
    residue:
      pdb=" N  AGLY H  41 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY H  41 " occ=0.50
    residue:
      pdb=" N  AGLY B  41 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY B  41 " occ=0.50
    residue:
      pdb=" N  AGLY I  41 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY I  41 " occ=0.50
    residue:
      pdb=" N  AGLY C  41 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY C  41 " occ=0.50
  Time building chain proxies: 0.57, per 1000 atoms: 0.51
  Number of scatterers: 1119
  At special positions: 0
  Unit cell: (65.57, 59.76, 29.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     258      8.00
     N     210      7.00
     C     651      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: 0.07
  Conformation dependent library (CDL) restraints added in 60.9 milliseconds
  

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  186

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 3 sheets defined
      0.0% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.02
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'G' and resid 43 through 45
    Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60
      removed outlier: 6.940A  pdb=" N   SER A  59 " --> pdb=" O   GLN B  60 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   SER B  59 " --> pdb=" O   GLN C  60 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 45
      removed outlier: 6.036A  pdb=" N   VAL B  43 " --> pdb=" O   ILE C  44 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    2 hydrogen bonds defined for protein.
    6 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: 0.09

  Time building geometry restraints manager: 0.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 234
        1.29 -     1.36: 207
        1.36 -     1.42: 72
        1.42 -     1.49: 206
        1.49 -     1.55: 406
  Bond restraints: 1125
  Sorted by residual:
  bond pdb=" CB  ASP B  42 "
       pdb=" CG  ASP B  42 "
    ideal  model  delta    sigma   weight residual
    1.516  1.467  0.049 2.50e-02 1.60e+03 3.83e+00
  bond pdb=" CA  ASP A  42 "
       pdb=" CB  ASP A  42 "
    ideal  model  delta    sigma   weight residual
    1.527  1.499  0.028 1.44e-02 4.82e+03 3.78e+00
  bond pdb=" CB  VAL H  43 "
       pdb=" CG2 VAL H  43 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.56e+00
  bond pdb=" CB  ASP A  42 "
       pdb=" CG  ASP A  42 "
    ideal  model  delta    sigma   weight residual
    1.516  1.470  0.046 2.50e-02 1.60e+03 3.43e+00
  bond pdb=" CB  VAL I  43 "
       pdb=" CG2 VAL I  43 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.46e+00
  ... (remaining 1120 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 1393
        2.05 -     4.10: 81
        4.10 -     6.15: 12
        6.15 -     8.20: 4
        8.20 -    10.25: 1
  Bond angle restraints: 1491
  Sorted by residual:
  angle pdb=" N   GLY I  38 "
        pdb=" CA  GLY I  38 "
        pdb=" C   GLY I  38 "
      ideal   model   delta    sigma   weight residual
     111.66  101.41   10.25 1.91e+00 2.74e-01 2.88e+01
  angle pdb=" N   GLY H  38 "
        pdb=" CA  GLY H  38 "
        pdb=" C   GLY H  38 "
      ideal   model   delta    sigma   weight residual
     111.66  104.88    6.78 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" N   THR D  34 "
        pdb=" CA  THR D  34 "
        pdb=" CB  THR D  34 "
      ideal   model   delta    sigma   weight residual
     112.78  107.40    5.38 1.53e+00 4.27e-01 1.23e+01
  angle pdb=" N   THR F  34 "
        pdb=" CA  THR F  34 "
        pdb=" CB  THR F  34 "
      ideal   model   delta    sigma   weight residual
     112.78  107.40    5.38 1.53e+00 4.27e-01 1.23e+01
  angle pdb=" N   THR E  34 "
        pdb=" CA  THR E  34 "
        pdb=" CB  THR E  34 "
      ideal   model   delta    sigma   weight residual
     112.78  107.40    5.38 1.53e+00 4.27e-01 1.23e+01
  ... (remaining 1486 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.35: 395
        8.35 -    16.70: 79
       16.70 -    25.04: 45
       25.04 -    33.39: 17
       33.39 -    41.74: 7
  Dihedral angle restraints: 543
    sinusoidal: 162
      harmonic: 381
  Sorted by residual:
  dihedral pdb=" CA  GLY F  33 "
           pdb=" C   GLY F  33 "
           pdb=" N   THR F  34 "
           pdb=" CA  THR F  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.47   20.53     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  GLY E  33 "
           pdb=" C   GLY E  33 "
           pdb=" N   THR E  34 "
           pdb=" CA  THR E  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.47   20.53     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  GLY D  33 "
           pdb=" C   GLY D  33 "
           pdb=" N   THR D  34 "
           pdb=" CA  THR D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.47   20.53     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 540 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 59
       0.034 -    0.067: 32
       0.067 -    0.100: 9
       0.100 -    0.134: 18
       0.134 -    0.167: 5
  Chirality restraints: 123
  Sorted by residual:
  chirality pdb=" CB  VAL I  43 "
            pdb=" CA  VAL I  43 "
            pdb=" CG1 VAL I  43 "
            pdb=" CG2 VAL I  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.98e-01
  chirality pdb=" CA  VAL B  43 "
            pdb=" N   VAL B  43 "
            pdb=" C   VAL B  43 "
            pdb=" CB  VAL B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  VAL A  46 "
            pdb=" N   VAL A  46 "
            pdb=" C   VAL A  46 "
            pdb=" CB  VAL A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.42e-01
  ... (remaining 120 not shown)

  Planarity restraints: 228
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E  34 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   THR E  34 "    0.032 2.00e-02 2.50e+03
        pdb=" O   THR E  34 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER E  35 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR F  34 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   THR F  34 "    0.032 2.00e-02 2.50e+03
        pdb=" O   THR F  34 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER F  35 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D  34 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   THR D  34 "    0.032 2.00e-02 2.50e+03
        pdb=" O   THR D  34 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER D  35 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 225 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.94: 630
        2.94 -     3.43: 837
        3.43 -     3.92: 1498
        3.92 -     4.41: 1657
        4.41 -     4.90: 3574
  Nonbonded interactions: 8196
  Sorted by model distance:
  nonbonded pdb=" N   ASP A  42 "
            pdb=" OD1 ASP A  42 "
     model   vdw
     2.456 3.120
  nonbonded pdb=" N   GLY I  38 "
            pdb=" O   GLY I  38 "
     model   vdw
     2.461 2.496
  nonbonded pdb=" N   ASP B  42 "
            pdb=" OD1 ASP B  42 "
     model   vdw
     2.485 3.120
  nonbonded pdb=" O   GLY E  33 "
            pdb=" N   SER E  35 "
     model   vdw
     2.517 3.120
  nonbonded pdb=" O   GLY F  33 "
            pdb=" N   SER F  35 "
     model   vdw
     2.517 3.120
  ... (remaining 8191 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 35 through 40 or resid 42 through 62))
  selection = (chain 'B' and (resid 35 through 40 or resid 42 through 62))
  selection = (chain 'C' and (resid 35 through 40 or resid 42 through 62))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'G' and (resid 35 through 40 or resid 42 through 54))
  selection = (chain 'H' and (resid 35 through 40 or resid 42 through 54))
  selection = (chain 'I' and (resid 35 through 40 or resid 42 through 54))
}

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=0.50 max=1.00 mean=0.98
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:             4.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.690
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
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      :  0.009   0.062   1125  Z= 0.444
  Angle     :  1.144  10.255   1491  Z= 0.620
  Chirality :  0.065   0.167    123
  Planarity :  0.004   0.018    228
  Dihedral  : 12.774  41.738    357
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.00 %
    Favored  : 80.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.82 (0.18), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.20 (0.13), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00857 ( 1125)
  covalent geometry    : angle       1.14425 ( 1491)
  hydrogen bonds       : bond        0.25715 (    2)
  hydrogen bonds       : angle       4.97711 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.023 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8116 (mp10) cc_final: 0.7738 (mp10)
REVERT: B   60 GLN cc_start: 0.7899 (mp10) cc_final: 0.7569 (mp10)
REVERT: C   44 ILE cc_start: 0.8139 (mt) cc_final: 0.7927 (mt)
REVERT: C   54 TYR cc_start: 0.5463 (m-80) cc_final: 0.5155 (m-80)
REVERT: C   60 GLN cc_start: 0.8095 (mp10) cc_final: 0.7499 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0204
  time to fit residues: 0.6681
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0670
   chunk 0 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.4569 r_free = 0.4569 target = 0.157929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.136798 restraints weight = 1425.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.4328 rms_B_bonded: 2.56
r_work: 0.4212 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.4092 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4085
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4085 r_free = 0.4085    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4085 r_free = 0.4085    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4085
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   1125  Z= 0.195
  Angle     :  0.997   9.766   1491  Z= 0.478
  Chirality :  0.060   0.166    123
  Planarity :  0.002   0.009    228
  Dihedral  :  5.877  17.603    195
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.36 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.81 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.34 (0.21), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.82 (0.16), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 1125)
  covalent geometry    : angle       0.99652 ( 1491)
  hydrogen bonds       : bond        0.04999 (    2)
  hydrogen bonds       : angle       4.29761 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.035 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8259 (mp10) cc_final: 0.7819 (mp10)
REVERT: B   60 GLN cc_start: 0.7840 (mp10) cc_final: 0.7590 (mp10)
REVERT: C   44 ILE cc_start: 0.8189 (mt) cc_final: 0.7943 (mt)
REVERT: C   54 TYR cc_start: 0.5842 (m-80) cc_final: 0.5532 (m-80)
REVERT: C   60 GLN cc_start: 0.8052 (mp10) cc_final: 0.7673 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0345
  time to fit residues: 0.9572
Evaluate side-chains
  23 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.154849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.133599 restraints weight = 1442.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.4271 rms_B_bonded: 2.40
r_work: 0.4157 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.4035 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4028
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4028 r_free = 0.4028    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4028 r_free = 0.4028    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4028
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   1125  Z= 0.213
  Angle     :  0.943   8.184   1491  Z= 0.456
  Chirality :  0.059   0.155    123
  Planarity :  0.002   0.008    228
  Dihedral  :  5.742  16.441    195
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.58 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.17 (0.24), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.70 (0.18), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR E  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 1125)
  covalent geometry    : angle       0.94348 ( 1491)
  hydrogen bonds       : bond        0.04328 (    2)
  hydrogen bonds       : angle       4.65832 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.025 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8273 (mp10) cc_final: 0.7831 (mp10)
REVERT: B   60 GLN cc_start: 0.7824 (mp10) cc_final: 0.7616 (mp10)
REVERT: C   44 ILE cc_start: 0.8172 (mt) cc_final: 0.7920 (mt)
REVERT: C   54 TYR cc_start: 0.5997 (m-80) cc_final: 0.5712 (m-80)
REVERT: C   60 GLN cc_start: 0.8118 (mp10) cc_final: 0.7739 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0195
  time to fit residues: 0.6289
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   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 = 0.4530 r_free = 0.4530 target = 0.155105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.133890 restraints weight = 1483.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.4267 rms_B_bonded: 2.50
r_work: 0.4152 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4029 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4026 r_free = 0.4026    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4026 r_free = 0.4026    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   1125  Z= 0.231
  Angle     :  0.924   6.968   1491  Z= 0.451
  Chirality :  0.057   0.152    123
  Planarity :  0.002   0.007    228
  Dihedral  :  5.727  16.181    195
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.36 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 18.52 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.99 (0.27), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.56 (0.20), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 1125)
  covalent geometry    : angle       0.92364 ( 1491)
  hydrogen bonds       : bond        0.04335 (    2)
  hydrogen bonds       : angle       4.90357 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.037 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8281 (mp10) cc_final: 0.7841 (mp10)
REVERT: B   60 GLN cc_start: 0.7850 (mp10) cc_final: 0.7632 (mp10)
REVERT: C   44 ILE cc_start: 0.7935 (mt) cc_final: 0.7679 (mt)
REVERT: C   54 TYR cc_start: 0.6001 (m-80) cc_final: 0.5707 (m-80)
REVERT: C   60 GLN cc_start: 0.8130 (mp10) cc_final: 0.7790 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0317
  time to fit residues: 0.9922
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0060
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
B  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.157951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.136467 restraints weight = 1431.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.4311 rms_B_bonded: 2.49
r_work: 0.4196 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4072 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4068 r_free = 0.4068    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4068 r_free = 0.4068    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   1125  Z= 0.175
  Angle     :  0.885   7.666   1491  Z= 0.421
  Chirality :  0.055   0.151    123
  Planarity :  0.002   0.006    228
  Dihedral  :  5.159  15.613    195
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.22 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.82 (0.29), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.43 (0.22), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 1125)
  covalent geometry    : angle       0.88494 ( 1491)
  hydrogen bonds       : bond        0.03435 (    2)
  hydrogen bonds       : angle       4.85789 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.023 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8254 (mp10) cc_final: 0.7854 (mp10)
REVERT: B   60 GLN cc_start: 0.7828 (mp10) cc_final: 0.7624 (mp10)
REVERT: C   44 ILE cc_start: 0.7825 (mt) cc_final: 0.7597 (mt)
REVERT: C   54 TYR cc_start: 0.6012 (m-80) cc_final: 0.5709 (m-80)
REVERT: C   60 GLN cc_start: 0.8083 (mp10) cc_final: 0.7757 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0239
  time to fit residues: 0.6899
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 14 optimal weight:    0.0030
   chunk 9 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.5590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.156706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.134803 restraints weight = 1428.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.4291 rms_B_bonded: 2.48
r_work: 0.4177 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4056 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   1125  Z= 0.185
  Angle     :  0.859   7.435   1491  Z= 0.413
  Chirality :  0.055   0.146    123
  Planarity :  0.002   0.006    228
  Dihedral  :  5.107  15.347    195
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.75 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.72 (0.31), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.36 (0.23), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 1125)
  covalent geometry    : angle       0.85869 ( 1491)
  hydrogen bonds       : bond        0.03478 (    2)
  hydrogen bonds       : angle       5.00275 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.036 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8286 (mp10) cc_final: 0.7872 (mp10)
REVERT: C   44 ILE cc_start: 0.7779 (mt) cc_final: 0.7565 (mt)
REVERT: C   60 GLN cc_start: 0.8112 (mp10) cc_final: 0.7781 (mp10)
  outliers start: 2
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0380
  time to fit residues: 1.1876
Evaluate side-chains
  23 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    0.2980
   chunk 12 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4565 r_free = 0.4565 target = 0.157656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.135290 restraints weight = 1426.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.4299 rms_B_bonded: 2.51
r_work: 0.4181 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.4060 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4055 r_free = 0.4055    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4055 r_free = 0.4055    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   1125  Z= 0.190
  Angle     :  0.880   7.347   1491  Z= 0.428
  Chirality :  0.054   0.147    123
  Planarity :  0.002   0.006    228
  Dihedral  :  5.047  15.509    195
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 24.69 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.70 (0.31), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.34 (0.24), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR I  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 1125)
  covalent geometry    : angle       0.88025 ( 1491)
  hydrogen bonds       : bond        0.03456 (    2)
  hydrogen bonds       : angle       5.10788 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.037 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8297 (mp10) cc_final: 0.7827 (mp10)
REVERT: C   44 ILE cc_start: 0.7703 (mt) cc_final: 0.7493 (mt)
REVERT: C   60 GLN cc_start: 0.8187 (mp10) cc_final: 0.7784 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0310
  time to fit residues: 0.8993
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0770
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7738

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

Flipped N/Q/H residues before XYZ refinement:
B  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.154949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.132512 restraints weight = 1402.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.4250 rms_B_bonded: 2.49
r_work: 0.4135 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.4012 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4012 r_free = 0.4012    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4012 r_free = 0.4012    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   1125  Z= 0.242
  Angle     :  0.919   6.905   1491  Z= 0.455
  Chirality :  0.055   0.144    123
  Planarity :  0.002   0.007    228
  Dihedral  :  5.508  15.947    195
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.36 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 24.69 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.75 (0.31), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.38 (0.24), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR I  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 1125)
  covalent geometry    : angle       0.91882 ( 1491)
  hydrogen bonds       : bond        0.03563 (    2)
  hydrogen bonds       : angle       5.29508 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.037 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8328 (mp10) cc_final: 0.7846 (mp10)
REVERT: C   44 ILE cc_start: 0.7900 (mt) cc_final: 0.7695 (mt)
REVERT: C   60 GLN cc_start: 0.8232 (mp10) cc_final: 0.7706 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0317
  time to fit residues: 0.9326
Evaluate side-chains
  24 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0370
   chunk 0 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6258

-------------------------------------------------------------------------------
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 = 0.4560 r_free = 0.4560 target = 0.157037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.134462 restraints weight = 1410.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.4290 rms_B_bonded: 2.51
r_work: 0.4169 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.4047 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4046 r_free = 0.4046    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4046 r_free = 0.4046    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   1125  Z= 0.205
  Angle     :  0.881   7.138   1491  Z= 0.432
  Chirality :  0.054   0.146    123
  Planarity :  0.002   0.006    228
  Dihedral  :  5.177  15.027    195
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.46 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.67 (0.32), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.32 (0.24), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR E  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 1125)
  covalent geometry    : angle       0.88098 ( 1491)
  hydrogen bonds       : bond        0.03652 (    2)
  hydrogen bonds       : angle       5.24150 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.022 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8312 (mp10) cc_final: 0.7843 (mp10)
REVERT: C   44 ILE cc_start: 0.7748 (mt) cc_final: 0.7537 (mt)
REVERT: C   60 GLN cc_start: 0.8205 (mp10) cc_final: 0.7707 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0209
  time to fit residues: 0.5572
Evaluate side-chains
  22 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 5 optimal weight:    0.0770
   chunk 2 optimal weight:    0.0770
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.4296

-------------------------------------------------------------------------------
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 = 0.4598 r_free = 0.4598 target = 0.159516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.137448 restraints weight = 1391.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.4344 rms_B_bonded: 2.47
r_work: 0.4224 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4102 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4099 r_free = 0.4099    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4099 r_free = 0.4099    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1125  Z= 0.159
  Angle     :  0.835   7.183   1491  Z= 0.404
  Chirality :  0.053   0.144    123
  Planarity :  0.001   0.006    228
  Dihedral  :  4.700  14.500    195
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 23.46 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.57 (0.32), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.24 (0.25), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR I  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 1125)
  covalent geometry    : angle       0.83509 ( 1491)
  hydrogen bonds       : bond        0.03220 (    2)
  hydrogen bonds       : angle       4.99354 (    6)

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

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

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  366 Ramachandran restraints generated.
    183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.034 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.8347 (mp10) cc_final: 0.7889 (mp10)
REVERT: B   37 GLN cc_start: 0.8054 (tt0) cc_final: 0.7545 (tm-30)
REVERT: C   44 ILE cc_start: 0.7568 (mt) cc_final: 0.7353 (mt)
REVERT: C   60 GLN cc_start: 0.8187 (mp10) cc_final: 0.7785 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0304
  time to fit residues: 0.8629
Evaluate side-chains
  22 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4560 r_free = 0.4560 target = 0.156576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.133742 restraints weight = 1403.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.4282 rms_B_bonded: 2.49
r_work: 0.4161 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.4041 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4040 r_free = 0.4040    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4040 r_free = 0.4040    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   1125  Z= 0.223
  Angle     :  0.879   6.943   1491  Z= 0.432
  Chirality :  0.055   0.144    123
  Planarity :  0.002   0.006    228
  Dihedral  :  5.285  15.425    195
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 24.69 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.64 (0.32), residues: 183
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.29 (0.24), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR F  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 1125)
  covalent geometry    : angle       0.87921 ( 1491)
  hydrogen bonds       : bond        0.03408 (    2)
  hydrogen bonds       : angle       5.25855 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 691.72 seconds
wall clock time: 12 minutes 35.55 seconds (755.55 seconds total)