Starting phenix.real_space_refine
on Fri Aug 22 16:47:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9opb_70687/08_2025/9opb_70687.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9opb_70687/08_2025/9opb_70687.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9opb_70687/08_2025/9opb_70687.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9opb_70687/08_2025/9opb_70687.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9opb_70687/08_2025/9opb_70687.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9opb_70687/08_2025/9opb_70687.map"
  }
  resolution = 3.6
  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=   0.004 sd=   0.039
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       5      5.16       5
     C    3740      2.51       5
     N    1205      2.21       5
     O    1195      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6145
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "M"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
    Chain: "O"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "P"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
    Chain: "Q"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "T"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "V"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
  Time building chain proxies: 1.39, per 1000 atoms: 0.23
  Number of scatterers: 6145
  At special positions: 0
  Unit cell: (115.5, 114.4, 110, 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       5     16.00
     O    1195      8.00
     N    1205      7.00
     C    3740      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: 0.43
  Conformation dependent library (CDL) restraints added in 134.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1450

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      96.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'M' and resid 33 through 43
    Processing helix  chain 'M' and resid 53 through 62
      removed outlier: 3.687A  pdb=" N   ASP M  62 " --> pdb=" O   ARG M  58 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 104 through 154
    Processing helix  chain 'N' and resid 51 through 65
    Processing helix  chain 'N' and resid 106 through 169
      removed outlier: 3.750A  pdb=" N   ASN N 124 " --> pdb=" O   GLY N 120 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 34 through 44
      removed outlier: 4.524A  pdb=" N   MET O  44 " --> pdb=" O   LEU O  40 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 53 through 62
    Processing helix  chain 'O' and resid 104 through 154
    Processing helix  chain 'P' and resid 51 through 65
    Processing helix  chain 'P' and resid 106 through 169
    Processing helix  chain 'Q' and resid 34 through 44
    Processing helix  chain 'Q' and resid 53 through 62
    Processing helix  chain 'Q' and resid 104 through 154
    Processing helix  chain 'R' and resid 51 through 65
    Processing helix  chain 'R' and resid 106 through 169
      removed outlier: 3.868A  pdb=" N   ASN R 124 " --> pdb=" O   GLY R 120 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 34 through 43
    Processing helix  chain 'S' and resid 53 through 62
    Processing helix  chain 'S' and resid 104 through 154
      removed outlier: 3.578A  pdb=" N   THR S 154 " --> pdb=" O   LEU S 150 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 51 through 65
    Processing helix  chain 'T' and resid 106 through 169
    Processing helix  chain 'U' and resid 34 through 43
    Processing helix  chain 'U' and resid 53 through 62
    Processing helix  chain 'U' and resid 104 through 154
    Processing helix  chain 'V' and resid 51 through 65
    Processing helix  chain 'V' and resid 106 through 169

    648 hydrogen bonds defined for protein.
    1944 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: 0.84

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2279
        1.34 -     1.46: 476
        1.46 -     1.57: 3395
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 6160
  Sorted by residual:
  bond pdb=" CB  GLU V 149 "
       pdb=" CG  GLU V 149 "
    ideal  model  delta    sigma   weight residual
    1.520  1.484  0.036 3.00e-02 1.11e+03 1.46e+00
  bond pdb=" CG  GLU V 149 "
       pdb=" CD  GLU V 149 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 1.01e+00
  bond pdb=" CB  GLU N 149 "
       pdb=" CG  GLU N 149 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.29e-01
  bond pdb=" N   GLU N 149 "
       pdb=" CA  GLU N 149 "
    ideal  model  delta    sigma   weight residual
    1.459  1.471 -0.012 1.25e-02 6.40e+03 9.07e-01
  bond pdb=" CB  ARG N 146 "
       pdb=" CG  ARG N 146 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 3.00e-02 1.11e+03 7.13e-01
  ... (remaining 6155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 8166
        1.48 -     2.96: 99
        2.96 -     4.44: 15
        4.44 -     5.92: 3
        5.92 -     7.39: 2
  Bond angle restraints: 8285
  Sorted by residual:
  angle pdb=" C   ARG V 148 "
        pdb=" N   GLU V 149 "
        pdb=" CA  GLU V 149 "
      ideal   model   delta    sigma   weight residual
     120.31  116.35    3.96 1.52e+00 4.33e-01 6.79e+00
  angle pdb=" CA  LEU V 143 "
        pdb=" CB  LEU V 143 "
        pdb=" CG  LEU V 143 "
      ideal   model   delta    sigma   weight residual
     116.30  123.69   -7.39 3.50e+00 8.16e-02 4.46e+00
  angle pdb=" CA  ASP R 147 "
        pdb=" CB  ASP R 147 "
        pdb=" CG  ASP R 147 "
      ideal   model   delta    sigma   weight residual
     112.60  114.67   -2.07 1.00e+00 1.00e+00 4.30e+00
  angle pdb=" C   ARG R 146 "
        pdb=" N   ASP R 147 "
        pdb=" CA  ASP R 147 "
      ideal   model   delta    sigma   weight residual
     120.68  117.19    3.49 1.70e+00 3.46e-01 4.23e+00
  angle pdb=" CA  LEU N 143 "
        pdb=" CB  LEU N 143 "
        pdb=" CG  LEU N 143 "
      ideal   model   delta    sigma   weight residual
     116.30  123.10   -6.80 3.50e+00 8.16e-02 3.77e+00
  ... (remaining 8280 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 3314
       17.39 -    34.79: 370
       34.79 -    52.18: 60
       52.18 -    69.58: 14
       69.58 -    86.97: 17
  Dihedral angle restraints: 3775
    sinusoidal: 1550
      harmonic: 2225
  Sorted by residual:
  dihedral pdb=" CB  GLU N 130 "
           pdb=" CG  GLU N 130 "
           pdb=" CD  GLU N 130 "
           pdb=" OE1 GLU N 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.97  -86.97     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  GLU N 145 "
           pdb=" CG  GLU N 145 "
           pdb=" CD  GLU N 145 "
           pdb=" OE1 GLU N 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.83  -85.83     1      3.00e+01 1.11e-03 9.89e+00
  dihedral pdb=" CB  GLU P 130 "
           pdb=" CG  GLU P 130 "
           pdb=" CD  GLU P 130 "
           pdb=" OE1 GLU P 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.74  -85.74     1      3.00e+01 1.11e-03 9.87e+00
  ... (remaining 3772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 707
       0.028 -    0.055: 170
       0.055 -    0.083: 85
       0.083 -    0.111: 9
       0.111 -    0.138: 4
  Chirality restraints: 975
  Sorted by residual:
  chirality pdb=" CA  ASP R 147 "
            pdb=" N   ASP R 147 "
            pdb=" C   ASP R 147 "
            pdb=" CB  ASP R 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CB  ILE N 114 "
            pdb=" CA  ILE N 114 "
            pdb=" CG1 ILE N 114 "
            pdb=" CG2 ILE N 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.12 2.00e-01 2.50e+01 3.66e-01
  chirality pdb=" CB  ILE S  53 "
            pdb=" CA  ILE S  53 "
            pdb=" CG1 ILE S  53 "
            pdb=" CG2 ILE S  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.53    0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 972 not shown)

  Planarity restraints: 1115
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU V 149 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.27e+00
        pdb=" CD  GLU V 149 "   -0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU V 149 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU V 149 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R 147 "    0.006 2.00e-02 2.50e+03   1.10e-02 1.22e+00
        pdb=" C   ASP R 147 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ASP R 147 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ARG R 148 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N 146 "    0.096 9.50e-02 1.11e+02   4.29e-02 1.14e+00
        pdb=" NE  ARG N 146 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  ARG N 146 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG N 146 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG N 146 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1112 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.97: 2735
        2.97 -     3.45: 7429
        3.45 -     3.93: 9754
        3.93 -     4.42: 10281
        4.42 -     4.90: 15619
  Nonbonded interactions: 45818
  Sorted by model distance:
  nonbonded pdb=" O   GLU N 145 "
            pdb=" OE1 GLU N 149 "
     model   vdw
     2.483 3.040
  nonbonded pdb=" O   GLN R 144 "
            pdb=" OD1 ASP R 147 "
     model   vdw
     2.553 3.040
  nonbonded pdb=" O   LEU O 125 "
            pdb=" OG1 THR O 128 "
     model   vdw
     2.603 3.040
  nonbonded pdb=" O   GLU V 145 "
            pdb=" OE1 GLU V 149 "
     model   vdw
     2.608 3.040
  nonbonded pdb=" N   ALA N 105 "
            pdb=" N   PHE N 106 "
     model   vdw
     2.638 2.560
  ... (remaining 45813 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 'M'
  selection = chain 'O'
  selection = chain 'Q'
  selection = chain 'S'
  selection = chain 'U'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'P'
  selection = chain 'R'
  selection = chain 'T'
  selection = chain 'V'
}

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 group one per residue
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:             7.760
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5750
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      :  0.002   0.036   6160  Z= 0.118
  Angle     :  0.438   7.394   8285  Z= 0.237
  Chirality :  0.031   0.138    975
  Planarity :  0.003   0.043   1115
  Dihedral  : 15.828  86.969   2325
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.27 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.54 (0.27), residues: 730
  helix:  4.18 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG V 146 
 TYR   0.013   0.001   TYR R  60 
 PHE   0.008   0.001   PHE U 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 6160)
  covalent geometry    : angle       0.43793 ( 8285)
  hydrogen bonds       : bond        0.07029 (  648)
  hydrogen bonds       : angle       3.30874 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 312
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  122 ILE cc_start: 0.6290 (tt) cc_final: 0.5995 (tt)
REVERT: O  108 THR cc_start: 0.4925 (p) cc_final: 0.4587 (t)
REVERT: Q  143 LEU cc_start: 0.5047 (mt) cc_final: 0.4318 (mt)
REVERT: R  132 LEU cc_start: 0.8831 (mp) cc_final: 0.8602 (mm)
REVERT: R  143 LEU cc_start: 0.7270 (mt) cc_final: 0.7031 (tp)
REVERT: S  143 LEU cc_start: 0.7576 (tt) cc_final: 0.6909 (mt)
REVERT: T   53 ILE cc_start: 0.7520 (mt) cc_final: 0.7318 (mt)
REVERT: U   60 TYR cc_start: 0.7131 (t80) cc_final: 0.6529 (t80)
REVERT: U  135 THR cc_start: 0.7829 (p) cc_final: 0.7603 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 312
  average time/residue: 0.1493
  time to fit residues: 53.5086
Evaluate side-chains
  141 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
M 115 ASN
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 123 ASN
V 115 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.100827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.096914 restraints weight = 45585.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.097448 restraints weight = 32333.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.097831 restraints weight = 24483.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.098046 restraints weight = 19762.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.098256 restraints weight = 16918.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6194
moved from start:          0.5540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6160  Z= 0.159
  Angle     :  0.647  11.675   8285  Z= 0.331
  Chirality :  0.037   0.216    975
  Planarity :  0.005   0.085   1115
  Dihedral  :  3.143  10.699    880
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 16.83 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.95 (0.26), residues: 730
  helix:  3.82 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG O 146 
 TYR   0.021   0.002   TYR R  60 
 PHE   0.012   0.001   PHE N 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6160)
  covalent geometry    : angle       0.64669 ( 8285)
  hydrogen bonds       : bond        0.04984 (  648)
  hydrogen bonds       : angle       3.58207 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 156
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   55 ASP cc_start: 0.7863 (t0) cc_final: 0.7544 (p0)
  outliers start: 32
  outliers final: 20
  residues processed: 174
  average time/residue: 0.1022
  time to fit residues: 21.9861
Evaluate side-chains
  149 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  128 THR
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain O residue  117 VAL
Chi-restraints excluded: chain O residue  129 ILE
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue   52 ASP
Chi-restraints excluded: chain R residue  122 ILE
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   53 ILE
Chi-restraints excluded: chain S residue  126 PHE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue   44 MET
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  125 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 66 optimal weight:   30.0000
   chunk 35 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 144 GLN
S 112 ASN
S 123 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.098117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.094917 restraints weight = 45045.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.094988 restraints weight = 39794.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.095333 restraints weight = 31100.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.095366 restraints weight = 25767.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.095411 restraints weight = 22625.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
moved from start:          0.6949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6160  Z= 0.153
  Angle     :  0.596   7.959   8285  Z= 0.312
  Chirality :  0.035   0.158    975
  Planarity :  0.004   0.069   1115
  Dihedral  :  3.165  12.044    880
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 22.70 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.58 (0.26), residues: 730
  helix:  3.59 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N 131 
 TYR   0.022   0.002   TYR R  60 
 PHE   0.014   0.001   PHE N 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6160)
  covalent geometry    : angle       0.59633 ( 8285)
  hydrogen bonds       : bond        0.05336 (  648)
  hydrogen bonds       : angle       3.60444 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  123 ASN cc_start: 0.6903 (m-40) cc_final: 0.6266 (m110)
  outliers start: 27
  outliers final: 15
  residues processed: 167
  average time/residue: 0.0909
  time to fit residues: 18.8786
Evaluate side-chains
  150 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue   52 ASP
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   57 VAL
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  125 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 2 optimal weight:   30.0000
   chunk 62 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 12 optimal weight:   30.0000
   chunk 47 optimal weight:    9.9990
   chunk 31 optimal weight:   50.0000
   overall best weight:    5.3588

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 144 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.096884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.093075 restraints weight = 44151.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.093567 restraints weight = 31709.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.093908 restraints weight = 23990.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.094153 restraints weight = 19517.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.094282 restraints weight = 16709.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6383
moved from start:          0.7720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6160  Z= 0.146
  Angle     :  0.619   9.734   8285  Z= 0.314
  Chirality :  0.035   0.147    975
  Planarity :  0.004   0.057   1115
  Dihedral  :  3.074  11.246    880
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.44 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.70 (0.26), residues: 730
  helix:  3.66 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG M 151 
 TYR   0.018   0.002   TYR R  60 
 PHE   0.008   0.001   PHE N 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6160)
  covalent geometry    : angle       0.61875 ( 8285)
  hydrogen bonds       : bond        0.05357 (  648)
  hydrogen bonds       : angle       3.57104 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V  119 GLU cc_start: 0.6102 (tm-30) cc_final: 0.5238 (tm-30)
  outliers start: 23
  outliers final: 15
  residues processed: 178
  average time/residue: 0.1027
  time to fit residues: 22.3792
Evaluate side-chains
  161 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue  143 LEU
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   53 ILE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue   44 MET
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  125 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 36 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 61 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   overall best weight:    5.7788

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

Flipped N/Q/H residues before XYZ refinement:
M 136 ASN
N 112 ASN
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.095830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.092139 restraints weight = 44845.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.092743 restraints weight = 30325.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.093122 restraints weight = 22044.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.093428 restraints weight = 17436.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.093613 restraints weight = 14613.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6427
moved from start:          0.8423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6160  Z= 0.151
  Angle     :  0.610   9.451   8285  Z= 0.317
  Chirality :  0.035   0.150    975
  Planarity :  0.004   0.061   1115
  Dihedral  :  3.135  12.446    880
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 24.92 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.48 (0.26), residues: 730
  helix:  3.53 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG R 146 
 TYR   0.017   0.002   TYR U  60 
 PHE   0.006   0.001   PHE N 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6160)
  covalent geometry    : angle       0.60999 ( 8285)
  hydrogen bonds       : bond        0.05596 (  648)
  hydrogen bonds       : angle       3.63066 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   53 ILE cc_start: 0.7297 (tp) cc_final: 0.7041 (mp)
REVERT: V   53 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7879 (mm)
  outliers start: 27
  outliers final: 17
  residues processed: 173
  average time/residue: 0.0991
  time to fit residues: 21.0225
Evaluate side-chains
  162 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  119 GLU
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue   53 ILE
Chi-restraints excluded: chain V residue  125 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 53 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 0 optimal weight:   40.0000
   chunk 37 optimal weight:   20.0000
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 20 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  54 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.094883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.091287 restraints weight = 43861.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.091889 restraints weight = 28875.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.092290 restraints weight = 20468.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.092566 restraints weight = 15768.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.092673 restraints weight = 12934.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6586
moved from start:          0.8855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6160  Z= 0.154
  Angle     :  0.658   9.611   8285  Z= 0.335
  Chirality :  0.037   0.237    975
  Planarity :  0.004   0.061   1115
  Dihedral  :  3.132  12.783    880
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 25.40 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.46 (0.26), residues: 730
  helix:  3.52 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 146 
 TYR   0.016   0.002   TYR U  60 
 PHE   0.006   0.001   PHE N 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6160)
  covalent geometry    : angle       0.65848 ( 8285)
  hydrogen bonds       : bond        0.05675 (  648)
  hydrogen bonds       : angle       3.67800 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   53 ILE cc_start: 0.7660 (tp) cc_final: 0.7394 (mp)
REVERT: T   54 ASN cc_start: 0.7191 (m110) cc_final: 0.6785 (t0)
REVERT: V  148 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6556 (tpp80)
  outliers start: 31
  outliers final: 20
  residues processed: 174
  average time/residue: 0.1143
  time to fit residues: 24.2082
Evaluate side-chains
  167 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   60 TYR
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  119 GLU
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  125 LEU
Chi-restraints excluded: chain V residue  136 ASN
Chi-restraints excluded: chain V residue  148 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 47 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 7 optimal weight:   20.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  43 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.094196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.090442 restraints weight = 45036.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.091055 restraints weight = 30271.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.091444 restraints weight = 21824.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.091680 restraints weight = 17011.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.091858 restraints weight = 14283.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6474
moved from start:          0.9260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6160  Z= 0.155
  Angle     :  0.653   9.166   8285  Z= 0.337
  Chirality :  0.037   0.269    975
  Planarity :  0.004   0.055   1115
  Dihedral  :  3.156  13.220    880
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 16.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 26.83 %
    Favored  : 68.25 %
  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 aren not related in a simple way.
  whole:  5.36 (0.26), residues: 730
  helix:  3.46 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 146 
 TYR   0.012   0.002   TYR Q  60 
 PHE   0.008   0.001   PHE O 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6160)
  covalent geometry    : angle       0.65297 ( 8285)
  hydrogen bonds       : bond        0.05799 (  648)
  hydrogen bonds       : angle       3.70919 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  108 THR cc_start: 0.4740 (p) cc_final: 0.4289 (t)
REVERT: Q   53 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7286 (mp)
REVERT: S  125 LEU cc_start: 0.7400 (pp) cc_final: 0.7141 (mt)
REVERT: T   54 ASN cc_start: 0.7136 (m110) cc_final: 0.6850 (t0)
REVERT: U  143 LEU cc_start: 0.7181 (tt) cc_final: 0.6839 (tt)
REVERT: V  148 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6462 (tpp80)
  outliers start: 31
  outliers final: 21
  residues processed: 171
  average time/residue: 0.1134
  time to fit residues: 23.5719
Evaluate side-chains
  164 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue   53 ILE
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   60 TYR
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  106 PHE
Chi-restraints excluded: chain T residue  119 GLU
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  125 LEU
Chi-restraints excluded: chain V residue  136 ASN
Chi-restraints excluded: chain V residue  148 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 13 optimal weight:   50.0000
   chunk 33 optimal weight:    6.9990
   chunk 24 optimal weight:   20.0000
   chunk 30 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.092899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.089139 restraints weight = 44874.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.089694 restraints weight = 30658.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.090104 restraints weight = 22597.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.090347 restraints weight = 17765.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.090540 restraints weight = 14951.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.9772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6160  Z= 0.167
  Angle     :  0.662   8.866   8285  Z= 0.347
  Chirality :  0.037   0.223    975
  Planarity :  0.005   0.064   1115
  Dihedral  :  3.221  13.028    880
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 27.94 %
    Favored  : 67.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.03 (0.26), residues: 730
  helix:  3.28 (0.16), residues: 725
  sheet:  None (None), residues: 0
  loop : -0.47 (1.39), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 146 
 TYR   0.013   0.002   TYR Q  60 
 PHE   0.008   0.001   PHE U 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6160)
  covalent geometry    : angle       0.66227 ( 8285)
  hydrogen bonds       : bond        0.06126 (  648)
  hydrogen bonds       : angle       3.87162 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 153
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   53 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7175 (mp)
REVERT: V  148 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6352 (tpp80)
  outliers start: 29
  outliers final: 21
  residues processed: 167
  average time/residue: 0.1085
  time to fit residues: 22.3426
Evaluate side-chains
  156 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue   53 ILE
Chi-restraints excluded: chain Q residue   57 VAL
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   60 TYR
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  106 PHE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  136 ASN
Chi-restraints excluded: chain V residue  148 ARG
Chi-restraints excluded: chain V residue  154 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 34 optimal weight:   20.0000
   chunk 10 optimal weight:   30.0000
   chunk 24 optimal weight:   20.0000
   chunk 63 optimal weight:    9.9990
   chunk 46 optimal weight:   40.0000
   chunk 60 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
N 123 ASN
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.092250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.088745 restraints weight = 45284.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.089278 restraints weight = 30609.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.089637 restraints weight = 22132.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.089864 restraints weight = 17315.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.089971 restraints weight = 14572.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6561
moved from start:          1.0246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6160  Z= 0.179
  Angle     :  0.715   9.149   8285  Z= 0.375
  Chirality :  0.038   0.154    975
  Planarity :  0.005   0.078   1115
  Dihedral  :  3.390  15.966    880
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 18.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 28.57 %
    Favored  : 66.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.75 (0.26), residues: 730
  helix:  3.10 (0.16), residues: 725
  sheet:  None (None), residues: 0
  loop : -0.12 (1.92), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG N 152 
 TYR   0.013   0.002   TYR Q  60 
 PHE   0.008   0.001   PHE U 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6160)
  covalent geometry    : angle       0.71473 ( 8285)
  hydrogen bonds       : bond        0.06380 (  648)
  hydrogen bonds       : angle       4.06467 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  121 TYR cc_start: 0.5798 (t80) cc_final: 0.5525 (t80)
REVERT: Q   53 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7192 (mp)
REVERT: V  148 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6762 (tpp80)
  outliers start: 31
  outliers final: 23
  residues processed: 160
  average time/residue: 0.1072
  time to fit residues: 21.3128
Evaluate side-chains
  156 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue   53 ILE
Chi-restraints excluded: chain Q residue   57 VAL
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain R residue  149 GLU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   60 TYR
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  106 PHE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  108 THR
Chi-restraints excluded: chain V residue  136 ASN
Chi-restraints excluded: chain V residue  148 ARG
Chi-restraints excluded: chain V residue  154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 56 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 70 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   chunk 43 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 29 optimal weight:    5.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.092836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.089207 restraints weight = 45297.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.089770 restraints weight = 30995.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.090058 restraints weight = 22484.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.090319 restraints weight = 18229.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.090510 restraints weight = 15489.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6561
moved from start:          1.0290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6160  Z= 0.169
  Angle     :  0.730  11.942   8285  Z= 0.378
  Chirality :  0.039   0.188    975
  Planarity :  0.005   0.081   1115
  Dihedral  :  3.355  15.829    880
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 31.59 %
    Favored  : 65.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.95 (0.26), residues: 730
  helix:  3.22 (0.16), residues: 725
  sheet:  None (None), residues: 0
  loop : -0.44 (1.97), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG N  58 
 TYR   0.013   0.002   TYR S 121 
 PHE   0.008   0.001   PHE N 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6160)
  covalent geometry    : angle       0.72998 ( 8285)
  hydrogen bonds       : bond        0.06235 (  648)
  hydrogen bonds       : angle       3.92842 ( 1944)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  121 TYR cc_start: 0.5657 (t80) cc_final: 0.5398 (t80)
REVERT: Q   53 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7178 (mp)
REVERT: V  148 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6680 (ttp80)
  outliers start: 20
  outliers final: 17
  residues processed: 156
  average time/residue: 0.1220
  time to fit residues: 22.9699
Evaluate side-chains
  150 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   42 ILE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue   53 ILE
Chi-restraints excluded: chain Q residue   57 VAL
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   60 TYR
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  106 PHE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  108 THR
Chi-restraints excluded: chain V residue  148 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 48 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   chunk 57 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 18 optimal weight:   20.0000
   chunk 11 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 34 optimal weight:   20.0000
   chunk 60 optimal weight:    6.9990
   overall best weight:    9.1990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.090886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.087216 restraints weight = 44285.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.087782 restraints weight = 30026.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.088210 restraints weight = 22100.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.088470 restraints weight = 17143.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.088673 restraints weight = 14216.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
moved from start:          1.0693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6160  Z= 0.196
  Angle     :  0.781  10.035   8285  Z= 0.410
  Chirality :  0.040   0.167    975
  Planarity :  0.005   0.076   1115
  Dihedral  :  3.531  16.656    880
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 30.32 %
    Favored  : 65.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.22 (0.26), residues: 730
  helix:  2.77 (0.16), residues: 725
  sheet:  None (None), residues: 0
  loop : -0.38 (2.06), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG N 152 
 TYR   0.017   0.002   TYR U 121 
 PHE   0.010   0.001   PHE U 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6160)
  covalent geometry    : angle       0.78070 ( 8285)
  hydrogen bonds       : bond        0.06810 (  648)
  hydrogen bonds       : angle       4.26386 ( 1944)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1301.35 seconds
wall clock time: 23 minutes 2.63 seconds (1382.63 seconds total)