Starting phenix.real_space_refine
on Wed Sep 17 04:48:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mga_48244/09_2025/9mga_48244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mga_48244/09_2025/9mga_48244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mga_48244/09_2025/9mga_48244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mga_48244/09_2025/9mga_48244.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mga_48244/09_2025/9mga_48244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mga_48244/09_2025/9mga_48244.map"
  }
  resolution = 2.85
  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=   0.002 sd=   0.033
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    3423      2.51       5
     N     525      2.21       5
     O     651      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 126 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4599
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "0"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 76
          Unusual residues: {'I7L': 1}
          Classifications: {'peptide': 7, 'undetermined': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1}
            Not linked:
              pdbres="I7L 0   1 "
              pdbres="PHE 0   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'I7L:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "1"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 67
          Unusual residues: {'I7L': 1}
          Classifications: {'peptide': 6, 'undetermined': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1}
            Not linked:
              pdbres="I7L 1   1 "
              pdbres="PHE 1   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'I7L:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "2"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 76
          Unusual residues: {'I7L': 1}
          Classifications: {'peptide': 7, 'undetermined': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1}
            Not linked:
              pdbres="I7L 2   1 "
              pdbres="PHE 2   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'I7L:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Restraints were copied for chains:
    3, 6, 9, AA, C, F, I, L, O, R, U, X, c, f, i, l, o, r, u, x, 4, 7,
    A, D, G, J, M, P, S, V, Y, a, d, g, j, m, p, s, v, y, 5, 8, B, E,
    H, K, N, Q, T, W, Z, b, e, h, k, n, q, t, w, z
  Time building chain proxies: 0.66, per 1000 atoms: 0.14
  Number of scatterers: 4599
  At special positions: 0
  Unit cell: (81.03, 82.14, 57.72, 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     651      8.00
     N     525      7.00
     C    3423      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=63, symmetry=0
  Number of additional bonds: simple=63, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 80.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  714

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...

    No hydrogen bonds 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: 0.00

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.16 -     1.27: 588
        1.27 -     1.38: 2216
        1.38 -     1.49: 892
        1.49 -     1.60: 1092
        1.60 -     1.71: 63
  Bond restraints: 4851
  Sorted by residual:
  bond pdb=" C02 I7L c   1 "
       pdb=" C04 I7L c   1 "
    ideal  model  delta    sigma   weight residual
    1.555  1.714 -0.159 2.00e-02 2.50e+03 6.30e+01
  bond pdb=" C02 I7L S   1 "
       pdb=" C04 I7L S   1 "
    ideal  model  delta    sigma   weight residual
    1.555  1.714 -0.159 2.00e-02 2.50e+03 6.30e+01
  bond pdb=" C02 I7L x   1 "
       pdb=" C04 I7L x   1 "
    ideal  model  delta    sigma   weight residual
    1.555  1.714 -0.159 2.00e-02 2.50e+03 6.30e+01
  bond pdb=" C02 I7L G   1 "
       pdb=" C04 I7L G   1 "
    ideal  model  delta    sigma   weight residual
    1.555  1.714 -0.159 2.00e-02 2.50e+03 6.29e+01
  bond pdb=" C02 I7L R   1 "
       pdb=" C04 I7L R   1 "
    ideal  model  delta    sigma   weight residual
    1.555  1.714 -0.159 2.00e-02 2.50e+03 6.29e+01
  ... (remaining 4846 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.16: 6132
        5.16 -    10.32: 189
       10.32 -    15.48: 21
       15.48 -    20.63: 21
       20.63 -    25.79: 63
  Bond angle restraints: 6426
  Sorted by residual:
  angle pdb=" C04 I7L n   1 "
        pdb=" C02 I7L n   1 "
        pdb=" O01 I7L n   1 "
      ideal   model   delta    sigma   weight residual
     115.75   89.96   25.79 3.00e+00 1.11e-01 7.39e+01
  angle pdb=" C04 I7L T   1 "
        pdb=" C02 I7L T   1 "
        pdb=" O01 I7L T   1 "
      ideal   model   delta    sigma   weight residual
     115.75   89.96   25.79 3.00e+00 1.11e-01 7.39e+01
  angle pdb=" C04 I7L 5   1 "
        pdb=" C02 I7L 5   1 "
        pdb=" O01 I7L 5   1 "
      ideal   model   delta    sigma   weight residual
     115.75   89.96   25.79 3.00e+00 1.11e-01 7.39e+01
  angle pdb=" C04 I7L h   1 "
        pdb=" C02 I7L h   1 "
        pdb=" O01 I7L h   1 "
      ideal   model   delta    sigma   weight residual
     115.75   89.97   25.78 3.00e+00 1.11e-01 7.38e+01
  angle pdb=" C04 I7L Q   1 "
        pdb=" C02 I7L Q   1 "
        pdb=" O01 I7L Q   1 "
      ideal   model   delta    sigma   weight residual
     115.75   89.98   25.77 3.00e+00 1.11e-01 7.38e+01
  ... (remaining 6421 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.13: 1764
       14.13 -    28.27: 273
       28.27 -    42.40: 63
       42.40 -    56.53: 84
       56.53 -    70.67: 21
  Dihedral angle restraints: 2205
    sinusoidal: 1071
      harmonic: 1134
  Sorted by residual:
  dihedral pdb=" N   PHE O   2 "
           pdb=" C   PHE O   2 "
           pdb=" CA  PHE O   2 "
           pdb=" CB  PHE O   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.94    9.86     0      2.50e+00 1.60e-01 1.56e+01
  dihedral pdb=" N   PHE L   2 "
           pdb=" C   PHE L   2 "
           pdb=" CA  PHE L   2 "
           pdb=" CB  PHE L   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.94    9.86     0      2.50e+00 1.60e-01 1.56e+01
  dihedral pdb=" N   PHE f   2 "
           pdb=" C   PHE f   2 "
           pdb=" CA  PHE f   2 "
           pdb=" CB  PHE f   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.94    9.86     0      2.50e+00 1.60e-01 1.55e+01
  ... (remaining 2202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 252
       0.054 -    0.107: 42
       0.107 -    0.161: 0
       0.161 -    0.215: 42
       0.215 -    0.268: 21
  Chirality restraints: 357
  Sorted by residual:
  chirality pdb=" CA  PHE I   2 "
            pdb=" N   PHE I   2 "
            pdb=" C   PHE I   2 "
            pdb=" CB  PHE I   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  PHE R   2 "
            pdb=" N   PHE R   2 "
            pdb=" C   PHE R   2 "
            pdb=" CB  PHE R   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  PHE F   2 "
            pdb=" N   PHE F   2 "
            pdb=" C   PHE F   2 "
            pdb=" CB  PHE F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.80e+00
  ... (remaining 354 not shown)

  Planarity restraints: 777
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE y   3 "   -0.020 2.00e-02 2.50e+03   2.16e-02 8.15e+00
        pdb=" CG  PHE y   3 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE y   3 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE y   3 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE y   3 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE y   3 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE y   3 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE p   3 "   -0.020 2.00e-02 2.50e+03   2.16e-02 8.13e+00
        pdb=" CG  PHE p   3 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE p   3 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE p   3 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE p   3 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE p   3 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE p   3 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE P   3 "   -0.020 2.00e-02 2.50e+03   2.15e-02 8.12e+00
        pdb=" CG  PHE P   3 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE P   3 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE P   3 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE P   3 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE P   3 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE P   3 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 774 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.02: 2592
        3.02 -     3.49: 2724
        3.49 -     3.96: 5947
        3.96 -     4.43: 8231
        4.43 -     4.90: 13054
  Nonbonded interactions: 32548
  Sorted by model distance:
  nonbonded pdb=" O   PHE P   2 "
            pdb=" O   PHE Y   3 "
     model   vdw
     2.556 3.040
  nonbonded pdb=" O   PHE 4   2 "
            pdb=" O   PHE d   3 "
     model   vdw
     2.556 3.040
  nonbonded pdb=" O   PHE 1   2 "
            pdb=" O   PHE a   3 "
     model   vdw
     2.556 3.040
  nonbonded pdb=" O   PHE 7   2 "
            pdb=" O   PHE g   3 "
     model   vdw
     2.556 3.040
  nonbonded pdb=" O   PHE A   2 "
            pdb=" O   PHE M   3 "
     model   vdw
     2.556 3.040
  ... (remaining 32543 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain '0' and resid 1 through 7)
  selection = chain '1'
  selection = (chain '2' and resid 1 through 7)
  selection = (chain '3' and resid 1 through 7)
  selection = chain '4'
  selection = (chain '5' and resid 1 through 7)
  selection = (chain '6' and resid 1 through 7)
  selection = chain '7'
  selection = (chain '8' and resid 1 through 7)
  selection = (chain '9' and resid 1 through 7)
  selection = chain 'A'
  selection = (chain 'AA' and resid 1 through 7)
  selection = (chain 'B' and resid 1 through 7)
  selection = (chain 'C' and resid 1 through 7)
  selection = chain 'D'
  selection = (chain 'E' and resid 1 through 7)
  selection = (chain 'F' and resid 1 through 7)
  selection = chain 'G'
  selection = (chain 'H' and resid 1 through 7)
  selection = (chain 'I' and resid 1 through 7)
  selection = chain 'J'
  selection = (chain 'K' and resid 1 through 7)
  selection = (chain 'L' and resid 1 through 7)
  selection = chain 'M'
  selection = (chain 'N' and resid 1 through 7)
  selection = (chain 'O' and resid 1 through 7)
  selection = chain 'P'
  selection = (chain 'Q' and resid 1 through 7)
  selection = (chain 'R' and resid 1 through 7)
  selection = chain 'S'
  selection = (chain 'T' and resid 1 through 7)
  selection = (chain 'U' and resid 1 through 7)
  selection = chain 'V'
  selection = (chain 'W' and resid 1 through 7)
  selection = (chain 'X' and resid 1 through 7)
  selection = chain 'Y'
  selection = (chain 'Z' and resid 1 through 7)
  selection = chain 'a'
  selection = (chain 'b' and resid 1 through 7)
  selection = (chain 'c' and resid 1 through 7)
  selection = chain 'd'
  selection = (chain 'e' and resid 1 through 7)
  selection = (chain 'f' and resid 1 through 7)
  selection = chain 'g'
  selection = (chain 'h' and resid 1 through 7)
  selection = (chain 'i' and resid 1 through 7)
  selection = chain 'j'
  selection = (chain 'k' and resid 1 through 7)
  selection = (chain 'l' and resid 1 through 7)
  selection = chain 'm'
  selection = (chain 'n' and resid 1 through 7)
  selection = (chain 'o' and resid 1 through 7)
  selection = chain 'p'
  selection = (chain 'q' and resid 1 through 7)
  selection = (chain 'r' and resid 1 through 7)
  selection = chain 's'
  selection = (chain 't' and resid 1 through 7)
  selection = (chain 'u' and resid 1 through 7)
  selection = chain 'v'
  selection = (chain 'w' and resid 1 through 7)
  selection = (chain 'x' and resid 1 through 7)
  selection = chain 'y'
  selection = (chain 'z' and resid 1 through 7)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.410
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.500
  Find NCS groups from input model:        0.150
  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:6.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
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      :  0.035   0.159   4914  Z= 1.867
  Angle     :  3.300  25.793   6426  Z= 1.434
  Chirality :  0.094   0.268    357
  Planarity :  0.016   0.062    777
  Dihedral  : 18.894  70.665   1491
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 11.76 %
    Favored  : 82.35 %
  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: -5.15 (0.19), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.92 (0.15), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR 1   7 
 PHE   0.047   0.011   PHE y   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.03489 ( 4851)
  covalent geometry    : angle       3.29981 ( 6426)
  Misc. bond           : bond        0.02035 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 32
  time to evaluate  : 0.108 
Fit side-chains
REVERT: D    7 TYR cc_start: 0.5495 (OUTLIER) cc_final: 0.5131 (m-80)
REVERT: M    7 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6702 (m-80)
REVERT: V    7 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6896 (m-80)
REVERT: 4    7 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7183 (m-80)
REVERT: 7    7 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.5946 (m-80)
REVERT: j    7 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.6029 (m-80)
  outliers start: 21
  outliers final: 3
  residues processed: 53
  average time/residue: 0.4041
  time to fit residues: 22.6391
Evaluate side-chains
  36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain M residue    7 TYR
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain s residue    7 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.6980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
E   8 GLN
H   8 GLN
K   8 GLN
N   8 GLN
T   8 GLN
W   8 GLN
Z   8 GLN
2   8 GLN
5   8 GLN
8   8 GLN
b   8 GLN
e   8 GLN
h   8 GLN
k   8 GLN
n   8 GLN
q   8 GLN
t   8 GLN
w   8 GLN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.056569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.045736 restraints weight = 11352.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.2500 rms_B_bonded: 2.44
r_work: 0.2397 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2279 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9011
moved from start:          0.5819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.135   0.725   4914  Z= 5.374
  Angle     :  4.627  31.782   6426  Z= 2.422
  Chirality :  0.286   0.722    357
  Planarity :  0.036   0.144    777
  Dihedral  : 24.214  84.677    627
  Min Nonbonded Distance : 1.758

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  2.38 %
    Allowed  : 18.03 %
    Favored  : 79.59 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  :  5.04 %
    Favored  : 87.11 %
  Cbeta Deviations :  8.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 6.80 %

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: -5.50 (0.29), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.19 (0.22), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.111   0.022   TYR I   7 
 PHE   0.123   0.026   PHE 7   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13585 ( 4851)
  covalent geometry    : angle       4.62693 ( 6426)
  Misc. bond           : bond        0.00967 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 53
  time to evaluate  : 0.168 
Fit side-chains
REVERT: J    6 GLN cc_start: 0.8797 (pt0) cc_final: 0.8585 (pt0)
REVERT: O    8 GLN cc_start: 0.8252 (mt0) cc_final: 0.7034 (tm-30)
REVERT: Q    8 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8202 (mp10)
REVERT: U    8 GLN cc_start: 0.7935 (mt0) cc_final: 0.6956 (tm-30)
REVERT: 2    8 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8343 (mp10)
REVERT: 3    8 GLN cc_start: 0.8054 (mt0) cc_final: 0.7195 (tm-30)
REVERT: 5    8 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8390 (mm110)
REVERT: 9    8 GLN cc_start: 0.7990 (mt0) cc_final: 0.6875 (tm-30)
REVERT: c    8 GLN cc_start: 0.8429 (mt0) cc_final: 0.7751 (tm-30)
REVERT: i    8 GLN cc_start: 0.8356 (mt0) cc_final: 0.7574 (tm-30)
REVERT: j    7 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6777 (m-80)
REVERT: m    7 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.6703 (m-80)
REVERT: y    6 GLN cc_start: 0.8841 (pt0) cc_final: 0.7848 (pp30)
  outliers start: 28
  outliers final: 16
  residues processed: 74
  average time/residue: 0.7944
  time to fit residues: 60.3426
Evaluate side-chains
  69 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 50
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 TYR
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain P residue    7 TYR
Chi-restraints excluded: chain Q residue    8 GLN
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain Y residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain a residue    7 TYR
Chi-restraints excluded: chain g residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain m residue    7 TYR
Chi-restraints excluded: chain o residue    8 GLN
Chi-restraints excluded: chain p residue    7 TYR
Chi-restraints excluded: chain s residue    7 TYR
Chi-restraints excluded: chain v residue    7 TYR
Chi-restraints excluded: chain y residue    7 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
E   8 GLN
N   8 GLN
T   8 GLN
a   6 GLN
h   8 GLN
k   8 GLN
p   6 GLN
q   8 GLN
s   6 GLN
w   8 GLN
z   8 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.056072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2507 r_free = 0.2507 target = 0.045249 restraints weight = 10993.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.2502 rms_B_bonded: 2.44
r_work: 0.2396 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2274 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9009
moved from start:          0.5925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.135   0.749   4914  Z= 5.380
  Angle     :  4.622  30.166   6426  Z= 2.438
  Chirality :  0.287   0.697    357
  Planarity :  0.037   0.157    777
  Dihedral  : 23.411  81.079    625
  Min Nonbonded Distance : 1.770

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 21.43 %
    Favored  : 78.23 %
  Rotamer:
    Outliers :  9.24 %
    Allowed  : 10.92 %
    Favored  : 79.83 %
  Cbeta Deviations :  9.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 12.70 %
    Twisted General : 7.82 %

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: -5.67 (0.31), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.32 (0.24), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.127   0.022   TYR I   7 
 PHE   0.124   0.027   PHE P   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13604 ( 4851)
  covalent geometry    : angle       4.62224 ( 6426)
  Misc. bond           : bond        0.00925 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 45
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8551 (pt0)
REVERT: L    8 GLN cc_start: 0.8122 (mt0) cc_final: 0.7565 (tm130)
REVERT: Q    8 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8395 (mp10)
REVERT: U    8 GLN cc_start: 0.7980 (mt0) cc_final: 0.7036 (tm-30)
REVERT: W    8 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8146 (mp10)
REVERT: 2    8 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7775 (mt0)
REVERT: 3    8 GLN cc_start: 0.8056 (mt0) cc_final: 0.7135 (tm-30)
REVERT: 6    8 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7514 (tm-30)
REVERT: 9    8 GLN cc_start: 0.8013 (mt0) cc_final: 0.6925 (tm-30)
REVERT: b    8 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7290 (mm-40)
REVERT: c    8 GLN cc_start: 0.8221 (mt0) cc_final: 0.7621 (tm-30)
REVERT: i    8 GLN cc_start: 0.8364 (mt0) cc_final: 0.7528 (tm-30)
REVERT: j    7 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6735 (m-80)
REVERT: l    8 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6499 (tm-30)
REVERT: m    7 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.6432 (m-80)
REVERT: n    8 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8688 (mm-40)
REVERT: w    8 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8292 (mm110)
REVERT: y    6 GLN cc_start: 0.8820 (pt0) cc_final: 0.7860 (pp30)
  outliers start: 33
  outliers final: 20
  residues processed: 71
  average time/residue: 0.7701
  time to fit residues: 56.1555
Evaluate side-chains
  75 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 45
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue    7 TYR
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain P residue    7 TYR
Chi-restraints excluded: chain Q residue    8 GLN
Chi-restraints excluded: chain R residue    5 PRO
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain W residue    8 GLN
Chi-restraints excluded: chain Y residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 2 residue    8 GLN
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 6 residue    8 GLN
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain a residue    7 TYR
Chi-restraints excluded: chain b residue    8 GLN
Chi-restraints excluded: chain g residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain l residue    8 GLN
Chi-restraints excluded: chain m residue    6 GLN
Chi-restraints excluded: chain m residue    7 TYR
Chi-restraints excluded: chain n residue    8 GLN
Chi-restraints excluded: chain o residue    8 GLN
Chi-restraints excluded: chain p residue    7 TYR
Chi-restraints excluded: chain s residue    7 TYR
Chi-restraints excluded: chain v residue    7 TYR
Chi-restraints excluded: chain y residue    5 PRO
Chi-restraints excluded: chain y residue    7 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
N   8 GLN
Q   8 GLN
a   6 GLN
k   8 GLN
p   6 GLN
q   8 GLN
z   8 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.056242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2509 r_free = 0.2509 target = 0.045334 restraints weight = 11310.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.2500 rms_B_bonded: 2.45
r_work: 0.2394 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2273 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9018
moved from start:          0.5966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.782   4914  Z= 5.389
  Angle     :  4.657  30.471   6426  Z= 2.461
  Chirality :  0.285   0.724    357
  Planarity :  0.037   0.159    777
  Dihedral  : 23.389  80.662    625
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  : 21.09 %
    Favored  : 77.89 %
  Rotamer:
    Outliers :  9.80 %
    Allowed  : 11.76 %
    Favored  : 78.43 %
  Cbeta Deviations :  9.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 12.70 %
    Twisted General : 7.82 %

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: -5.76 (0.30), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.38 (0.23), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.129   0.022   TYR I   7 
 PHE   0.126   0.027   PHE P   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13643 ( 4851)
  covalent geometry    : angle       4.65704 ( 6426)
  Misc. bond           : bond        0.00910 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 45
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8593 (pt0)
REVERT: L    8 GLN cc_start: 0.8375 (mt0) cc_final: 0.7588 (tm130)
REVERT: U    8 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7096 (tm-30)
REVERT: W    8 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7526 (mp10)
REVERT: 2    8 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8428 (mp10)
REVERT: 3    8 GLN cc_start: 0.8229 (mt0) cc_final: 0.7340 (tm-30)
REVERT: 6    8 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7531 (tm-30)
REVERT: 9    8 GLN cc_start: 0.8068 (mt0) cc_final: 0.6997 (tm-30)
REVERT: c    8 GLN cc_start: 0.8227 (mt0) cc_final: 0.7765 (tt0)
REVERT: i    8 GLN cc_start: 0.8394 (mt0) cc_final: 0.7531 (tm-30)
REVERT: j    7 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6734 (m-80)
REVERT: l    8 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.6541 (tm-30)
REVERT: m    7 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.6592 (m-80)
REVERT: n    8 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7453 (mm-40)
REVERT: p    7 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7962 (m-80)
REVERT: q    6 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.9151 (tt0)
REVERT: y    6 GLN cc_start: 0.8815 (pt0) cc_final: 0.7931 (pp30)
  outliers start: 35
  outliers final: 20
  residues processed: 70
  average time/residue: 0.7825
  time to fit residues: 56.2240
Evaluate side-chains
  76 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 45
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue    7 TYR
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain P residue    7 TYR
Chi-restraints excluded: chain U residue    8 GLN
Chi-restraints excluded: chain V residue    6 GLN
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain W residue    8 GLN
Chi-restraints excluded: chain Y residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 2 residue    8 GLN
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 6 residue    8 GLN
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain a residue    7 TYR
Chi-restraints excluded: chain g residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain l residue    8 GLN
Chi-restraints excluded: chain m residue    6 GLN
Chi-restraints excluded: chain m residue    7 TYR
Chi-restraints excluded: chain n residue    8 GLN
Chi-restraints excluded: chain o residue    8 GLN
Chi-restraints excluded: chain p residue    7 TYR
Chi-restraints excluded: chain q residue    6 GLN
Chi-restraints excluded: chain s residue    7 TYR
Chi-restraints excluded: chain v residue    7 TYR
Chi-restraints excluded: chain y residue    5 PRO
Chi-restraints excluded: chain y residue    7 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
N   8 GLN
a   6 GLN
k   8 GLN
p   6 GLN
q   8 GLN
z   8 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.056111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2505 r_free = 0.2505 target = 0.045127 restraints weight = 11223.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.2500 rms_B_bonded: 2.48
r_work: 0.2394 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2273 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9012
moved from start:          0.5986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.135   0.752   4914  Z= 5.385
  Angle     :  4.650  30.406   6426  Z= 2.453
  Chirality :  0.287   0.726    357
  Planarity :  0.037   0.159    777
  Dihedral  : 23.394  80.787    625
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  : 21.77 %
    Favored  : 77.55 %
  Rotamer:
    Outliers : 11.20 %
    Allowed  : 12.32 %
    Favored  : 76.47 %
  Cbeta Deviations :  9.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 12.70 %
    Twisted General : 8.16 %

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: -5.75 (0.31), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.38 (0.23), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.130   0.022   TYR I   7 
 PHE   0.125   0.027   PHE P   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13632 ( 4851)
  covalent geometry    : angle       4.64973 ( 6426)
  Misc. bond           : bond        0.00902 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 45
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8559 (pt0)
REVERT: L    8 GLN cc_start: 0.8364 (mt0) cc_final: 0.7612 (tm130)
REVERT: Q    8 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8550 (mp10)
REVERT: U    8 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6957 (tm-30)
REVERT: W    8 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7574 (mp10)
REVERT: 2    8 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7575 (mt0)
REVERT: 3    8 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7381 (tm-30)
REVERT: 6    8 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7512 (tm-30)
REVERT: 9    8 GLN cc_start: 0.8059 (mt0) cc_final: 0.6975 (tm-30)
REVERT: b    8 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7276 (mm-40)
REVERT: c    8 GLN cc_start: 0.8223 (mt0) cc_final: 0.7758 (tt0)
REVERT: i    8 GLN cc_start: 0.8376 (mt0) cc_final: 0.7496 (tm-30)
REVERT: j    7 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6790 (m-80)
REVERT: l    8 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.6595 (tm-30)
REVERT: m    7 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.6586 (m-80)
REVERT: p    7 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7859 (m-80)
REVERT: q    6 GLN cc_start: 0.9440 (OUTLIER) cc_final: 0.9165 (tt0)
REVERT: y    6 GLN cc_start: 0.8810 (pt0) cc_final: 0.7934 (pp30)
  outliers start: 40
  outliers final: 21
  residues processed: 72
  average time/residue: 0.8329
  time to fit residues: 61.5219
Evaluate side-chains
  79 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 45
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue    7 TYR
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain M residue    6 GLN
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain P residue    7 TYR
Chi-restraints excluded: chain Q residue    8 GLN
Chi-restraints excluded: chain U residue    8 GLN
Chi-restraints excluded: chain V residue    6 GLN
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain W residue    8 GLN
Chi-restraints excluded: chain Y residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 2 residue    8 GLN
Chi-restraints excluded: chain 3 residue    8 GLN
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 6 residue    8 GLN
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain a residue    7 TYR
Chi-restraints excluded: chain b residue    8 GLN
Chi-restraints excluded: chain g residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain l residue    8 GLN
Chi-restraints excluded: chain m residue    6 GLN
Chi-restraints excluded: chain m residue    7 TYR
Chi-restraints excluded: chain o residue    8 GLN
Chi-restraints excluded: chain p residue    7 TYR
Chi-restraints excluded: chain q residue    6 GLN
Chi-restraints excluded: chain s residue    7 TYR
Chi-restraints excluded: chain v residue    7 TYR
Chi-restraints excluded: chain y residue    5 PRO
Chi-restraints excluded: chain y residue    7 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
N   8 GLN
a   6 GLN
k   8 GLN
p   6 GLN
q   8 GLN
z   8 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.056116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.045185 restraints weight = 11507.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.2501 rms_B_bonded: 2.47
r_work: 0.2394 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2274 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9017
moved from start:          0.5994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.777   4914  Z= 5.388
  Angle     :  4.661  30.422   6426  Z= 2.462
  Chirality :  0.287   0.727    357
  Planarity :  0.037   0.159    777
  Dihedral  : 23.454  81.073    625
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  : 21.77 %
    Favored  : 77.21 %
  Rotamer:
    Outliers : 11.76 %
    Allowed  : 12.04 %
    Favored  : 76.19 %
  Cbeta Deviations :  8.96 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 12.70 %
    Twisted General : 8.16 %

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: -5.76 (0.31), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.39 (0.23), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.133   0.022   TYR I   7 
 PHE   0.125   0.027   PHE P   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13643 ( 4851)
  covalent geometry    : angle       4.66098 ( 6426)
  Misc. bond           : bond        0.00898 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 46
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8564 (pt0)
REVERT: L    8 GLN cc_start: 0.8354 (mt0) cc_final: 0.7530 (tm130)
REVERT: Q    8 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8614 (mp10)
REVERT: U    8 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7065 (tm-30)
REVERT: W    8 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7575 (mp10)
REVERT: 2    8 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7588 (mt0)
REVERT: 3    8 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7376 (tm-30)
REVERT: 6    8 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7521 (tm-30)
REVERT: 8    8 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.7569 (mt0)
REVERT: 9    8 GLN cc_start: 0.8051 (mt0) cc_final: 0.6975 (tm-30)
REVERT: c    8 GLN cc_start: 0.8224 (mt0) cc_final: 0.7764 (tt0)
REVERT: d    7 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6952 (m-80)
REVERT: i    8 GLN cc_start: 0.8379 (mt0) cc_final: 0.7509 (tm-30)
REVERT: j    7 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6795 (m-80)
REVERT: l    8 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.6610 (tm-30)
REVERT: m    7 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.6618 (m-80)
REVERT: n    8 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7322 (mm-40)
REVERT: p    7 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7964 (m-80)
REVERT: q    6 GLN cc_start: 0.9437 (OUTLIER) cc_final: 0.9160 (tt0)
REVERT: y    6 GLN cc_start: 0.8802 (pt0) cc_final: 0.7933 (pp30)
  outliers start: 42
  outliers final: 22
  residues processed: 76
  average time/residue: 0.8517
  time to fit residues: 66.4059
Evaluate side-chains
  83 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 46
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue    7 TYR
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain M residue    6 GLN
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain P residue    7 TYR
Chi-restraints excluded: chain Q residue    8 GLN
Chi-restraints excluded: chain U residue    8 GLN
Chi-restraints excluded: chain V residue    6 GLN
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain W residue    8 GLN
Chi-restraints excluded: chain Y residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 2 residue    8 GLN
Chi-restraints excluded: chain 3 residue    8 GLN
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 6 residue    8 GLN
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain 8 residue    8 GLN
Chi-restraints excluded: chain a residue    7 TYR
Chi-restraints excluded: chain d residue    7 TYR
Chi-restraints excluded: chain g residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain l residue    8 GLN
Chi-restraints excluded: chain m residue    6 GLN
Chi-restraints excluded: chain m residue    7 TYR
Chi-restraints excluded: chain n residue    8 GLN
Chi-restraints excluded: chain o residue    6 GLN
Chi-restraints excluded: chain o residue    8 GLN
Chi-restraints excluded: chain p residue    7 TYR
Chi-restraints excluded: chain q residue    6 GLN
Chi-restraints excluded: chain s residue    7 TYR
Chi-restraints excluded: chain v residue    7 TYR
Chi-restraints excluded: chain y residue    5 PRO
Chi-restraints excluded: chain y residue    7 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
N   8 GLN
a   6 GLN
p   6 GLN
q   8 GLN
z   8 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.056255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2510 r_free = 0.2510 target = 0.045304 restraints weight = 11385.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.2502 rms_B_bonded: 2.46
r_work: 0.2398 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2276 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9016
moved from start:          0.6000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.775   4914  Z= 5.387
  Angle     :  4.661  30.413   6426  Z= 2.463
  Chirality :  0.287   0.732    357
  Planarity :  0.037   0.159    777
  Dihedral  : 23.462  80.589    625
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  : 22.11 %
    Favored  : 77.21 %
  Rotamer:
    Outliers : 11.20 %
    Allowed  : 11.48 %
    Favored  : 77.31 %
  Cbeta Deviations :  8.96 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 12.70 %
    Twisted General : 7.82 %

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: -5.77 (0.31), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.39 (0.23), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.131   0.022   TYR I   7 
 PHE   0.125   0.027   PHE P   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13641 ( 4851)
  covalent geometry    : angle       4.66078 ( 6426)
  Misc. bond           : bond        0.00901 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 45
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8561 (pt0)
REVERT: L    8 GLN cc_start: 0.8352 (mt0) cc_final: 0.7535 (tm130)
REVERT: Q    8 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8571 (mp10)
REVERT: U    8 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7026 (tm-30)
REVERT: W    8 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7584 (mp10)
REVERT: 2    8 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7554 (mt0)
REVERT: 3    8 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7383 (tm-30)
REVERT: 6    8 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7506 (tm-30)
REVERT: 9    8 GLN cc_start: 0.8046 (mt0) cc_final: 0.6961 (tm-30)
REVERT: b    8 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7243 (mm-40)
REVERT: c    8 GLN cc_start: 0.8201 (mt0) cc_final: 0.7747 (tt0)
REVERT: i    8 GLN cc_start: 0.8378 (mt0) cc_final: 0.7503 (tm-30)
REVERT: j    7 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6797 (m-80)
REVERT: l    8 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.6608 (tm-30)
REVERT: m    7 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6600 (m-80)
REVERT: p    7 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7872 (m-80)
REVERT: q    6 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9160 (tt0)
REVERT: y    6 GLN cc_start: 0.8803 (pt0) cc_final: 0.7956 (pp30)
  outliers start: 40
  outliers final: 21
  residues processed: 71
  average time/residue: 0.7978
  time to fit residues: 58.2060
Evaluate side-chains
  79 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 45
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue    7 TYR
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain P residue    7 TYR
Chi-restraints excluded: chain Q residue    8 GLN
Chi-restraints excluded: chain S residue    6 GLN
Chi-restraints excluded: chain U residue    8 GLN
Chi-restraints excluded: chain V residue    6 GLN
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain W residue    8 GLN
Chi-restraints excluded: chain Y residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 2 residue    8 GLN
Chi-restraints excluded: chain 3 residue    8 GLN
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 6 residue    8 GLN
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain a residue    7 TYR
Chi-restraints excluded: chain b residue    8 GLN
Chi-restraints excluded: chain g residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain l residue    8 GLN
Chi-restraints excluded: chain m residue    6 GLN
Chi-restraints excluded: chain m residue    7 TYR
Chi-restraints excluded: chain o residue    6 GLN
Chi-restraints excluded: chain o residue    8 GLN
Chi-restraints excluded: chain p residue    7 TYR
Chi-restraints excluded: chain q residue    6 GLN
Chi-restraints excluded: chain s residue    7 TYR
Chi-restraints excluded: chain v residue    7 TYR
Chi-restraints excluded: chain y residue    5 PRO
Chi-restraints excluded: chain y residue    7 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
N   8 GLN
a   6 GLN
p   6 GLN
q   8 GLN
z   8 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.056239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2510 r_free = 0.2510 target = 0.045287 restraints weight = 11531.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.2502 rms_B_bonded: 2.47
r_work: 0.2397 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2276 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9016
moved from start:          0.6002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.782   4914  Z= 5.389
  Angle     :  4.664  30.411   6426  Z= 2.463
  Chirality :  0.287   0.734    357
  Planarity :  0.037   0.158    777
  Dihedral  : 23.470  80.983    625
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  : 22.11 %
    Favored  : 77.21 %
  Rotamer:
    Outliers : 11.48 %
    Allowed  : 10.36 %
    Favored  : 78.15 %
  Cbeta Deviations :  8.96 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 12.70 %
    Twisted General : 8.16 %

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: -5.79 (0.31), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.40 (0.23), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.132   0.022   TYR I   7 
 PHE   0.125   0.027   PHE P   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13647 ( 4851)
  covalent geometry    : angle       4.66392 ( 6426)
  Misc. bond           : bond        0.00885 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 46
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8566 (pt0)
REVERT: L    8 GLN cc_start: 0.8350 (mt0) cc_final: 0.7502 (tm130)
REVERT: P    6 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8467 (pt0)
REVERT: Q    8 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8604 (mp10)
REVERT: U    8 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7049 (tm-30)
REVERT: W    8 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7571 (mp10)
REVERT: 2    8 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7556 (mt0)
REVERT: 3    8 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7398 (tm-30)
REVERT: 6    8 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7504 (tm-30)
REVERT: 8    8 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.7609 (mt0)
REVERT: 9    8 GLN cc_start: 0.8043 (mt0) cc_final: 0.6966 (tm-30)
REVERT: b    8 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7243 (mm-40)
REVERT: i    8 GLN cc_start: 0.8377 (mt0) cc_final: 0.7498 (tm-30)
REVERT: j    7 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6789 (m-80)
REVERT: l    8 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.6606 (tm-30)
REVERT: m    7 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.6594 (m-80)
REVERT: n    8 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7418 (mm-40)
REVERT: p    7 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7971 (m-80)
REVERT: q    6 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9162 (tt0)
REVERT: y    6 GLN cc_start: 0.8802 (pt0) cc_final: 0.7962 (pp30)
  outliers start: 41
  outliers final: 22
  residues processed: 74
  average time/residue: 0.8039
  time to fit residues: 61.1264
Evaluate side-chains
  84 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 46
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue    7 TYR
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain M residue    6 GLN
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain P residue    7 TYR
Chi-restraints excluded: chain Q residue    8 GLN
Chi-restraints excluded: chain S residue    6 GLN
Chi-restraints excluded: chain U residue    8 GLN
Chi-restraints excluded: chain V residue    6 GLN
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain W residue    8 GLN
Chi-restraints excluded: chain Y residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 2 residue    8 GLN
Chi-restraints excluded: chain 3 residue    8 GLN
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 6 residue    8 GLN
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain 8 residue    8 GLN
Chi-restraints excluded: chain a residue    7 TYR
Chi-restraints excluded: chain b residue    8 GLN
Chi-restraints excluded: chain g residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain l residue    8 GLN
Chi-restraints excluded: chain m residue    6 GLN
Chi-restraints excluded: chain m residue    7 TYR
Chi-restraints excluded: chain n residue    8 GLN
Chi-restraints excluded: chain o residue    6 GLN
Chi-restraints excluded: chain o residue    8 GLN
Chi-restraints excluded: chain p residue    7 TYR
Chi-restraints excluded: chain q residue    6 GLN
Chi-restraints excluded: chain s residue    7 TYR
Chi-restraints excluded: chain v residue    7 TYR
Chi-restraints excluded: chain y residue    5 PRO
Chi-restraints excluded: chain y residue    7 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
N   8 GLN
a   6 GLN
p   6 GLN
q   8 GLN
z   8 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.056116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.045105 restraints weight = 11298.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.2500 rms_B_bonded: 2.49
r_work: 0.2393 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2271 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9012
moved from start:          0.6005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.781   4914  Z= 5.389
  Angle     :  4.663  30.406   6426  Z= 2.464
  Chirality :  0.287   0.735    357
  Planarity :  0.037   0.159    777
  Dihedral  : 23.469  80.736    625
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  : 22.11 %
    Favored  : 77.21 %
  Rotamer:
    Outliers : 11.76 %
    Allowed  : 10.08 %
    Favored  : 78.15 %
  Cbeta Deviations :  8.96 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 12.70 %
    Twisted General : 7.82 %

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: -5.79 (0.31), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.41 (0.23), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.132   0.022   TYR I   7 
 PHE   0.125   0.027   PHE P   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13646 ( 4851)
  covalent geometry    : angle       4.66309 ( 6426)
  Misc. bond           : bond        0.00911 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 45
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8567 (pt0)
REVERT: L    8 GLN cc_start: 0.8359 (mt0) cc_final: 0.7497 (tm130)
REVERT: P    6 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8486 (pt0)
REVERT: Q    8 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8580 (mp10)
REVERT: U    8 GLN cc_start: 0.7976 (tt0) cc_final: 0.6921 (tm-30)
REVERT: W    8 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7576 (mp10)
REVERT: 2    8 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7563 (mt0)
REVERT: 3    8 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7401 (tm-30)
REVERT: 6    8 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7488 (tm-30)
REVERT: 8    8 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.7596 (mt0)
REVERT: 9    8 GLN cc_start: 0.8044 (mt0) cc_final: 0.6952 (tm-30)
REVERT: b    8 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7247 (mm-40)
REVERT: i    8 GLN cc_start: 0.8387 (mt0) cc_final: 0.7490 (tm-30)
REVERT: j    7 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6783 (m-80)
REVERT: l    8 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.6603 (tm-30)
REVERT: m    7 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6582 (m-80)
REVERT: p    7 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7961 (m-80)
REVERT: q    6 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.9170 (tt0)
REVERT: y    6 GLN cc_start: 0.8810 (pt0) cc_final: 0.7953 (pp30)
  outliers start: 42
  outliers final: 24
  residues processed: 73
  average time/residue: 0.8516
  time to fit residues: 63.7309
Evaluate side-chains
  83 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 45
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue    7 TYR
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain M residue    6 GLN
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain P residue    7 TYR
Chi-restraints excluded: chain Q residue    8 GLN
Chi-restraints excluded: chain S residue    6 GLN
Chi-restraints excluded: chain V residue    6 GLN
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain W residue    8 GLN
Chi-restraints excluded: chain Y residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 2 residue    8 GLN
Chi-restraints excluded: chain 3 residue    8 GLN
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 6 residue    8 GLN
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain 8 residue    8 GLN
Chi-restraints excluded: chain a residue    7 TYR
Chi-restraints excluded: chain b residue    6 GLN
Chi-restraints excluded: chain b residue    8 GLN
Chi-restraints excluded: chain g residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain l residue    8 GLN
Chi-restraints excluded: chain m residue    6 GLN
Chi-restraints excluded: chain m residue    7 TYR
Chi-restraints excluded: chain o residue    6 GLN
Chi-restraints excluded: chain o residue    8 GLN
Chi-restraints excluded: chain p residue    7 TYR
Chi-restraints excluded: chain q residue    6 GLN
Chi-restraints excluded: chain s residue    7 TYR
Chi-restraints excluded: chain v residue    6 GLN
Chi-restraints excluded: chain v residue    7 TYR
Chi-restraints excluded: chain y residue    5 PRO
Chi-restraints excluded: chain y residue    7 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
N   8 GLN
a   6 GLN
p   6 GLN
q   8 GLN
z   8 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.056078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2507 r_free = 0.2507 target = 0.045146 restraints weight = 11452.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.2503 rms_B_bonded: 2.47
r_work: 0.2396 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2274 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9017
moved from start:          0.6009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.779   4914  Z= 5.389
  Angle     :  4.667  30.403   6426  Z= 2.464
  Chirality :  0.288   0.735    357
  Planarity :  0.037   0.158    777
  Dihedral  : 23.474  80.860    625
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  : 22.11 %
    Favored  : 77.21 %
  Rotamer:
    Outliers : 10.64 %
    Allowed  : 11.20 %
    Favored  : 78.15 %
  Cbeta Deviations :  8.96 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 12.70 %
    Twisted General : 7.82 %

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: -5.81 (0.31), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.42 (0.23), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.132   0.022   TYR I   7 
 PHE   0.125   0.027   PHE P   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13646 ( 4851)
  covalent geometry    : angle       4.66692 ( 6426)
  Misc. bond           : bond        0.00884 (   63)

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

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

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  588 Ramachandran restraints generated.
    294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 45
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8567 (pt0)
REVERT: L    8 GLN cc_start: 0.8359 (mt0) cc_final: 0.7504 (tm130)
REVERT: P    6 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8489 (pt0)
REVERT: Q    8 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8576 (mp10)
REVERT: U    8 GLN cc_start: 0.7978 (tt0) cc_final: 0.6940 (tm-30)
REVERT: W    8 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7582 (mp10)
REVERT: 2    8 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7568 (mt0)
REVERT: 3    8 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7405 (tm-30)
REVERT: 6    8 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7498 (tm-30)
REVERT: 8    8 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.7618 (mt0)
REVERT: 9    8 GLN cc_start: 0.8049 (mt0) cc_final: 0.6975 (tm-30)
REVERT: b    8 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7263 (mm-40)
REVERT: i    8 GLN cc_start: 0.8387 (mt0) cc_final: 0.7495 (tm-30)
REVERT: j    7 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6793 (m-80)
REVERT: l    8 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.6709 (tm-30)
REVERT: m    7 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.6593 (m-80)
REVERT: p    7 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7969 (m-80)
REVERT: q    6 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9164 (tt0)
REVERT: y    6 GLN cc_start: 0.8804 (pt0) cc_final: 0.7959 (pp30)
  outliers start: 38
  outliers final: 22
  residues processed: 72
  average time/residue: 0.8376
  time to fit residues: 61.8310
Evaluate side-chains
  81 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 45
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue    7 TYR
Chi-restraints excluded: chain D residue    7 TYR
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain J residue    7 TYR
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain P residue    7 TYR
Chi-restraints excluded: chain Q residue    8 GLN
Chi-restraints excluded: chain S residue    6 GLN
Chi-restraints excluded: chain V residue    6 GLN
Chi-restraints excluded: chain V residue    7 TYR
Chi-restraints excluded: chain W residue    8 GLN
Chi-restraints excluded: chain Y residue    7 TYR
Chi-restraints excluded: chain 1 residue    7 TYR
Chi-restraints excluded: chain 2 residue    8 GLN
Chi-restraints excluded: chain 3 residue    8 GLN
Chi-restraints excluded: chain 4 residue    7 TYR
Chi-restraints excluded: chain 6 residue    8 GLN
Chi-restraints excluded: chain 7 residue    7 TYR
Chi-restraints excluded: chain 8 residue    8 GLN
Chi-restraints excluded: chain a residue    7 TYR
Chi-restraints excluded: chain b residue    6 GLN
Chi-restraints excluded: chain b residue    8 GLN
Chi-restraints excluded: chain g residue    7 TYR
Chi-restraints excluded: chain j residue    7 TYR
Chi-restraints excluded: chain l residue    8 GLN
Chi-restraints excluded: chain m residue    6 GLN
Chi-restraints excluded: chain m residue    7 TYR
Chi-restraints excluded: chain o residue    6 GLN
Chi-restraints excluded: chain o residue    8 GLN
Chi-restraints excluded: chain p residue    7 TYR
Chi-restraints excluded: chain q residue    6 GLN
Chi-restraints excluded: chain s residue    7 TYR
Chi-restraints excluded: chain v residue    7 TYR
Chi-restraints excluded: chain y residue    5 PRO
Chi-restraints excluded: chain y residue    7 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
N   8 GLN
a   6 GLN
p   6 GLN
q   8 GLN
v   6 GLN
z   8 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.056094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.045084 restraints weight = 11381.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.2500 rms_B_bonded: 2.50
r_work: 0.2394 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2272 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9012
moved from start:          0.6010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.781   4914  Z= 5.389
  Angle     :  4.664  30.399   6426  Z= 2.464
  Chirality :  0.287   0.735    357
  Planarity :  0.037   0.159    777
  Dihedral  : 23.471  80.797    625
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  : 22.11 %
    Favored  : 77.21 %
  Rotamer:
    Outliers : 10.36 %
    Allowed  : 11.20 %
    Favored  : 78.43 %
  Cbeta Deviations :  8.96 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 12.70 %
    Twisted General : 7.82 %

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: -5.81 (0.31), residues: 294
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.42 (0.23), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.132   0.022   TYR I   7 
 PHE   0.125   0.027   PHE P   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.13646 ( 4851)
  covalent geometry    : angle       4.66431 ( 6426)
  Misc. bond           : bond        0.00910 (   63)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1505.88 seconds
wall clock time: 26 minutes 22.96 seconds (1582.96 seconds total)