Starting phenix.real_space_refine
on Tue Jan 13 09:58:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zch_14631/01_2026/7zch_14631.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zch_14631/01_2026/7zch_14631.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zch_14631/01_2026/7zch_14631.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zch_14631/01_2026/7zch_14631.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zch_14631/01_2026/7zch_14631.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zch_14631/01_2026/7zch_14631.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    1520      2.51       5
     N     453      2.21       5
     O     464      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2468
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1194
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 2, 'TRANS': 144}
    Chain: "A"
      Number of atoms: 1274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1274
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 2, 'TRANS': 156}
  Time building chain proxies: 0.73, per 1000 atoms: 0.30
  Number of scatterers: 2468
  At special positions: 0
  Unit cell: (123.084, 140.968, 46.288, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O     464      8.00
     N     453      7.00
     C    1520      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.16
  Conformation dependent library (CDL) restraints added in 83.9 milliseconds
  

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  596

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 0 sheets defined
      93.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.03
  Creating SS restraints...
    Processing helix  chain 'B' and resid 10 through 51
      removed outlier: 3.692A  pdb=" N   ARG B  20 " --> pdb=" O   ARG B  16 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LEU B  36 " --> pdb=" O   GLU B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 115
      removed outlier: 3.784A  pdb=" N   ILE B  61 " --> pdb=" O   ASP B  57 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   LYS B  94 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER B  95 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 151
      removed outlier: 3.958A  pdb=" N   ILE B 122 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE B 147 " --> pdb=" O   MET B 143 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   MET B 151 " --> pdb=" O   ILE B 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 54
      removed outlier: 3.580A  pdb=" N   LYS A  22 " --> pdb=" O   GLU A  18 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A  24 " --> pdb=" O   SER A  20 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS A  25 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ARG A  46 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER A  47 " --> pdb=" O   LYS A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 116
      removed outlier: 3.961A  pdb=" N   ILE A  61 " --> pdb=" O   LYS A  57 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL A  62 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 149
    Processing helix  chain 'A' and resid 154 through 169
      removed outlier: 4.467A  pdb=" N   ALA A 161 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLU A 162 " --> pdb=" O   GLU A 158 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   MET A 163 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE A 168 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)

    237 hydrogen bonds defined for protein.
    711 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.23

  Time building geometry restraints manager: 0.23 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 842
        1.34 -     1.46: 125
        1.46 -     1.57: 1451
        1.57 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 2479
  Sorted by residual:
  bond pdb=" CG  GLN A  94 "
       pdb=" CD  GLN A  94 "
    ideal  model  delta    sigma   weight residual
    1.516  1.475  0.041 2.50e-02 1.60e+03 2.67e+00
  bond pdb=" CG  ARG B  27 "
       pdb=" CD  ARG B  27 "
    ideal  model  delta    sigma   weight residual
    1.520  1.481  0.039 3.00e-02 1.11e+03 1.73e+00
  bond pdb=" CB  MET A 151 "
       pdb=" CG  MET A 151 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.07e+00
  bond pdb=" CA  GLN A  94 "
       pdb=" CB  GLN A  94 "
    ideal  model  delta    sigma   weight residual
    1.528  1.512  0.016 1.66e-02 3.63e+03 9.18e-01
  bond pdb=" CB  MET B 113 "
       pdb=" CG  MET B 113 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 3.00e-02 1.11e+03 6.76e-01
  ... (remaining 2474 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 3065
        1.39 -     2.78: 177
        2.78 -     4.17: 29
        4.17 -     5.55: 11
        5.55 -     6.94: 5
  Bond angle restraints: 3287
  Sorted by residual:
  angle pdb=" CA  GLN A  94 "
        pdb=" CB  GLN A  94 "
        pdb=" CG  GLN A  94 "
      ideal   model   delta    sigma   weight residual
     114.10  107.16    6.94 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" C   GLY B  54 "
        pdb=" N   GLN B  55 "
        pdb=" CA  GLN B  55 "
      ideal   model   delta    sigma   weight residual
     121.54  127.79   -6.25 1.91e+00 2.74e-01 1.07e+01
  angle pdb=" CA  ARG A  24 "
        pdb=" CB  ARG A  24 "
        pdb=" CG  ARG A  24 "
      ideal   model   delta    sigma   weight residual
     114.10  120.23   -6.13 2.00e+00 2.50e-01 9.41e+00
  angle pdb=" C   ILE A  23 "
        pdb=" N   ARG A  24 "
        pdb=" CA  ARG A  24 "
      ideal   model   delta    sigma   weight residual
     121.58  115.95    5.63 1.95e+00 2.63e-01 8.35e+00
  angle pdb=" C   ILE B 125 "
        pdb=" N   MET B 126 "
        pdb=" CA  MET B 126 "
      ideal   model   delta    sigma   weight residual
     120.29  123.95   -3.66 1.42e+00 4.96e-01 6.65e+00
  ... (remaining 3282 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 1422
       17.91 -    35.83: 165
       35.83 -    53.74: 41
       53.74 -    71.65: 8
       71.65 -    89.56: 5
  Dihedral angle restraints: 1641
    sinusoidal: 739
      harmonic: 902
  Sorted by residual:
  dihedral pdb=" CA  MET B  56 "
           pdb=" C   MET B  56 "
           pdb=" N   ASP B  57 "
           pdb=" CA  ASP B  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.61  -20.39     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  GLN B  55 "
           pdb=" C   GLN B  55 "
           pdb=" N   MET B  56 "
           pdb=" CA  MET B  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.39   18.61     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  GLU B  32 "
           pdb=" C   GLU B  32 "
           pdb=" N   ARG B  33 "
           pdb=" CA  ARG B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.24   16.76     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 1638 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 233
       0.031 -    0.062: 85
       0.062 -    0.093: 35
       0.093 -    0.124: 13
       0.124 -    0.155: 4
  Chirality restraints: 370
  Sorted by residual:
  chirality pdb=" CA  ARG A  24 "
            pdb=" N   ARG A  24 "
            pdb=" C   ARG A  24 "
            pdb=" CB  ARG A  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.01e-01
  chirality pdb=" CA  GLN B  55 "
            pdb=" N   GLN B  55 "
            pdb=" C   GLN B  55 "
            pdb=" CB  GLN B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" CB  ILE A  37 "
            pdb=" CA  ILE A  37 "
            pdb=" CG1 ILE A  37 "
            pdb=" CG2 ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.77   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 367 not shown)

  Planarity restraints: 423
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  28 "   -0.009 2.00e-02 2.50e+03   1.74e-02 3.03e+00
        pdb=" C   GLU B  28 "    0.030 2.00e-02 2.50e+03
        pdb=" O   GLU B  28 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU B  29 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  11 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO A  12 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A  12 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  12 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 129 "   -0.005 2.00e-02 2.50e+03   1.01e-02 1.79e+00
        pdb=" CG  PHE B 129 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 129 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 129 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 129 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 129 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 129 "    0.000 2.00e-02 2.50e+03
  ... (remaining 420 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 437
        2.77 -     3.31: 2778
        3.31 -     3.84: 3983
        3.84 -     4.37: 4455
        4.37 -     4.90: 7204
  Nonbonded interactions: 18857
  Sorted by model distance:
  nonbonded pdb=" O   ALA A  52 "
            pdb=" NZ  LYS A  57 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   VAL A  44 "
            pdb=" OG  SER A  47 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   MET A 111 "
            pdb=" NE2 GLN A 115 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   ARG B 115 "
            pdb=" NZ  LYS B 118 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" ND2 ASN B 114 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.297 3.120
  ... (remaining 18852 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             27.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.950
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2479  Z= 0.191
  Angle     :  0.791   6.943   3287  Z= 0.432
  Chirality :  0.043   0.155    370
  Planarity :  0.005   0.051    423
  Dihedral  : 16.618  89.563   1045
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.49), residues: 302
  helix:  1.20 (0.31), residues: 275
  sheet:  None (None), residues: 0
  loop : -2.17 (1.28), residues: 27

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG A  24 
 TYR   0.006   0.001   TYR B  72 
 PHE   0.022   0.005   PHE B 129 
 TRP   0.016   0.004   TRP A  19 
 HIS   0.000   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 2479)
  covalent geometry    : angle       0.79147 ( 3287)
  hydrogen bonds       : bond        0.13234 (  237)
  hydrogen bonds       : angle       5.25769 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.7975 (m-30) cc_final: 0.7732 (m-30)
REVERT: B   34 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7890 (tp40)
REVERT: B   37 GLU cc_start: 0.8152 (mp0) cc_final: 0.7882 (mp0)
REVERT: B   64 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7588 (mmpt)
REVERT: B   66 LEU cc_start: 0.9237 (tp) cc_final: 0.8860 (mt)
REVERT: B   80 ARG cc_start: 0.8207 (ttt-90) cc_final: 0.7850 (ttm110)
REVERT: B   97 ASN cc_start: 0.8748 (t0) cc_final: 0.8338 (t0)
REVERT: B  119 LEU cc_start: 0.8539 (mm) cc_final: 0.8266 (mm)
REVERT: B  130 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7504 (mm-30)
REVERT: B  142 MET cc_start: 0.7747 (ptt) cc_final: 0.7010 (tmm)
REVERT: A   20 SER cc_start: 0.8956 (t) cc_final: 0.8594 (p)
REVERT: A   41 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7039 (mt-10)
REVERT: A   46 ARG cc_start: 0.8317 (ttm110) cc_final: 0.8019 (ttp-110)
REVERT: A   57 LYS cc_start: 0.7278 (mmtt) cc_final: 0.6943 (pttt)
REVERT: A   65 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8531 (mmtt)
REVERT: A   67 MET cc_start: 0.8114 (tpp) cc_final: 0.7813 (tpt)
REVERT: A   76 LYS cc_start: 0.9156 (ttpt) cc_final: 0.8804 (tttm)
REVERT: A  132 LYS cc_start: 0.8491 (tttt) cc_final: 0.8005 (ttmm)
REVERT: A  142 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7040 (mm-30)
REVERT: A  157 MET cc_start: 0.7568 (tmm) cc_final: 0.7332 (ttm)
REVERT: A  162 GLU cc_start: 0.6918 (pm20) cc_final: 0.6257 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1025
  time to fit residues: 23.7497
Evaluate side-chains
  191 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 27 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.114226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.104372 restraints weight = 6030.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.106445 restraints weight = 3073.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.107864 restraints weight = 1870.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.108735 restraints weight = 1285.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.109353 restraints weight = 973.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2479  Z= 0.177
  Angle     :  0.742   7.114   3287  Z= 0.388
  Chirality :  0.045   0.169    370
  Planarity :  0.005   0.041    423
  Dihedral  :  4.209  23.063    332
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 21.32 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.48), residues: 302
  helix:  1.87 (0.30), residues: 282
  sheet:  None (None), residues: 0
  loop : -3.08 (1.42), residues: 20

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  33 
 TYR   0.005   0.002   TYR B  72 
 PHE   0.003   0.001   PHE B 129 
 TRP   0.014   0.003   TRP A  19 
 HIS   0.000   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 2479)
  covalent geometry    : angle       0.74230 ( 3287)
  hydrogen bonds       : bond        0.05433 (  237)
  hydrogen bonds       : angle       4.20440 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 201
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8062 (tp30) cc_final: 0.7799 (tp30)
REVERT: B   26 MET cc_start: 0.8200 (mtp) cc_final: 0.7496 (mtp)
REVERT: B   30 ASP cc_start: 0.7875 (m-30) cc_final: 0.7444 (m-30)
REVERT: B   37 GLU cc_start: 0.8161 (mp0) cc_final: 0.7874 (mp0)
REVERT: B   64 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7624 (mmtt)
REVERT: B   74 ARG cc_start: 0.5985 (mmt180) cc_final: 0.5207 (mmt180)
REVERT: B   80 ARG cc_start: 0.8169 (ttt-90) cc_final: 0.7815 (ttm110)
REVERT: B   97 ASN cc_start: 0.8699 (t0) cc_final: 0.8223 (t0)
REVERT: B  119 LEU cc_start: 0.8433 (mm) cc_final: 0.8233 (tp)
REVERT: B  130 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7403 (mm-30)
REVERT: B  131 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7677 (ttp-170)
REVERT: B  142 MET cc_start: 0.8081 (ptt) cc_final: 0.7189 (tmm)
REVERT: B  151 MET cc_start: 0.6267 (tmm) cc_final: 0.4442 (ptp)
REVERT: A   39 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7727 (ttp-110)
REVERT: A   57 LYS cc_start: 0.7357 (mmtt) cc_final: 0.7059 (pttt)
REVERT: A   67 MET cc_start: 0.8062 (tpp) cc_final: 0.7734 (tpt)
REVERT: A   76 LYS cc_start: 0.9294 (ttpt) cc_final: 0.8879 (tttm)
REVERT: A  132 LYS cc_start: 0.8541 (tttt) cc_final: 0.8071 (ttmm)
REVERT: A  142 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7240 (mm-30)
REVERT: A  158 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7265 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 203
  average time/residue: 0.0927
  time to fit residues: 20.7442
Evaluate side-chains
  201 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 194
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  108 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  18 ASN
A  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.113487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.103825 restraints weight = 6106.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.105816 restraints weight = 3121.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.107129 restraints weight = 1889.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.107925 restraints weight = 1296.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.108572 restraints weight = 1000.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2479  Z= 0.157
  Angle     :  0.691   8.579   3287  Z= 0.354
  Chirality :  0.043   0.170    370
  Planarity :  0.004   0.024    423
  Dihedral  :  3.964  21.701    332
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 24.63 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.01 (0.48), residues: 302
  helix:  2.34 (0.30), residues: 275
  sheet:  None (None), residues: 0
  loop : -1.92 (1.32), residues: 27

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  68 
 TYR   0.005   0.001   TYR B  72 
 PHE   0.003   0.001   PHE B 129 
 TRP   0.018   0.004   TRP A  19 
 HIS   0.001   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 2479)
  covalent geometry    : angle       0.69144 ( 3287)
  hydrogen bonds       : bond        0.05095 (  237)
  hydrogen bonds       : angle       3.94803 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8135 (tp30) cc_final: 0.7564 (tp30)
REVERT: B   14 LEU cc_start: 0.9072 (mm) cc_final: 0.8851 (mm)
REVERT: B   17 GLN cc_start: 0.8211 (pt0) cc_final: 0.7316 (pt0)
REVERT: B   18 ASN cc_start: 0.8296 (t160) cc_final: 0.8072 (t0)
REVERT: B   19 GLN cc_start: 0.8136 (tp40) cc_final: 0.7894 (tp40)
REVERT: B   26 MET cc_start: 0.8384 (mtp) cc_final: 0.7827 (mtp)
REVERT: B   30 ASP cc_start: 0.7953 (m-30) cc_final: 0.7422 (m-30)
REVERT: B   33 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8411 (ttp-170)
REVERT: B   37 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7897 (mp0)
REVERT: B   40 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8315 (tm-30)
REVERT: B   74 ARG cc_start: 0.5846 (mmt180) cc_final: 0.4996 (mtm-85)
REVERT: B   80 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.7928 (ttm110)
REVERT: B  131 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7546 (ttp-170)
REVERT: B  142 MET cc_start: 0.8138 (ptt) cc_final: 0.7334 (tmm)
REVERT: B  151 MET cc_start: 0.6394 (tmm) cc_final: 0.4533 (ptm)
REVERT: A   17 ASN cc_start: 0.8622 (m110) cc_final: 0.8331 (m110)
REVERT: A   57 LYS cc_start: 0.7406 (mmtt) cc_final: 0.7192 (pttt)
REVERT: A   67 MET cc_start: 0.8024 (tpp) cc_final: 0.7816 (mmm)
REVERT: A   76 LYS cc_start: 0.9311 (ttpt) cc_final: 0.8952 (tttm)
REVERT: A  109 GLU cc_start: 0.8425 (tp30) cc_final: 0.7973 (tp30)
REVERT: A  119 LYS cc_start: 0.7934 (tptm) cc_final: 0.7663 (mmmt)
REVERT: A  132 LYS cc_start: 0.8590 (tttt) cc_final: 0.8130 (ttmm)
REVERT: A  142 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7253 (mm-30)
REVERT: A  159 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8123 (mm-30)
REVERT: A  162 GLU cc_start: 0.6986 (pm20) cc_final: 0.6269 (tt0)
  outliers start: 18
  outliers final: 8
  residues processed: 201
  average time/residue: 0.0954
  time to fit residues: 21.0355
Evaluate side-chains
  203 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 194
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  160 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 10 optimal weight:    0.1980
   chunk 5 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0770
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.113946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.104390 restraints weight = 6133.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.106398 restraints weight = 3079.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.107761 restraints weight = 1854.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.108674 restraints weight = 1258.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.109265 restraints weight = 942.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.4618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2479  Z= 0.139
  Angle     :  0.684   9.821   3287  Z= 0.342
  Chirality :  0.042   0.166    370
  Planarity :  0.003   0.024    423
  Dihedral  :  3.925  22.330    332
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 27.57 %
    Favored  : 66.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.28 (0.49), residues: 302
  helix:  2.52 (0.31), residues: 275
  sheet:  None (None), residues: 0
  loop : -1.84 (1.35), residues: 27

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 167 
 TYR   0.007   0.001   TYR B  72 
 PHE   0.010   0.001   PHE B 129 
 TRP   0.012   0.003   TRP A  19 
 HIS   0.000   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2479)
  covalent geometry    : angle       0.68422 ( 3287)
  hydrogen bonds       : bond        0.04922 (  237)
  hydrogen bonds       : angle       3.83801 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 202
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8111 (tp30) cc_final: 0.7530 (tp30)
REVERT: B   14 LEU cc_start: 0.9094 (mm) cc_final: 0.8860 (mm)
REVERT: B   17 GLN cc_start: 0.8270 (pt0) cc_final: 0.7311 (pt0)
REVERT: B   19 GLN cc_start: 0.8156 (tp40) cc_final: 0.7933 (tp40)
REVERT: B   26 MET cc_start: 0.8294 (mtp) cc_final: 0.7697 (mtp)
REVERT: B   30 ASP cc_start: 0.8023 (m-30) cc_final: 0.7455 (m-30)
REVERT: B   33 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8272 (ttp-170)
REVERT: B   37 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7809 (mp0)
REVERT: B   40 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8344 (tm-30)
REVERT: B   42 LYS cc_start: 0.8346 (tptp) cc_final: 0.8100 (tptp)
REVERT: B   74 ARG cc_start: 0.5591 (mmt180) cc_final: 0.4691 (mtm-85)
REVERT: B   80 ARG cc_start: 0.8218 (ttt-90) cc_final: 0.7900 (ttm110)
REVERT: B  123 GLN cc_start: 0.7994 (tt0) cc_final: 0.7677 (tt0)
REVERT: B  131 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7531 (ttp-170)
REVERT: B  142 MET cc_start: 0.8020 (ptt) cc_final: 0.7309 (tmm)
REVERT: B  151 MET cc_start: 0.6275 (tmm) cc_final: 0.4352 (ptm)
REVERT: A   17 ASN cc_start: 0.8664 (m110) cc_final: 0.8379 (m110)
REVERT: A   76 LYS cc_start: 0.9302 (ttpt) cc_final: 0.8944 (tttm)
REVERT: A  119 LYS cc_start: 0.7758 (tptm) cc_final: 0.7509 (mmmt)
REVERT: A  124 GLN cc_start: 0.8837 (mm110) cc_final: 0.8624 (mm-40)
REVERT: A  132 LYS cc_start: 0.8609 (tttt) cc_final: 0.8142 (ttmm)
REVERT: A  142 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7308 (mm-30)
  outliers start: 15
  outliers final: 11
  residues processed: 204
  average time/residue: 0.1017
  time to fit residues: 22.7731
Evaluate side-chains
  208 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 196
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   53 GLN
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  160 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 28 optimal weight:    0.0030
   chunk 6 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  18 ASN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  33 GLN
A 124 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.113553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.103763 restraints weight = 6104.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.105807 restraints weight = 3089.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.107205 restraints weight = 1869.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.108110 restraints weight = 1276.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.108391 restraints weight = 953.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2479  Z= 0.146
  Angle     :  0.666   9.998   3287  Z= 0.342
  Chirality :  0.042   0.174    370
  Planarity :  0.003   0.025    423
  Dihedral  :  3.851  23.176    332
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 27.57 %
    Favored  : 66.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.25 (0.48), residues: 302
  helix:  2.50 (0.30), residues: 275
  sheet:  None (None), residues: 0
  loop : -1.85 (1.36), residues: 27

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 167 
 TYR   0.008   0.001   TYR B  72 
 PHE   0.006   0.001   PHE B  76 
 TRP   0.012   0.003   TRP A  19 
 HIS   0.001   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 2479)
  covalent geometry    : angle       0.66601 ( 3287)
  hydrogen bonds       : bond        0.04846 (  237)
  hydrogen bonds       : angle       3.84908 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 200
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8189 (tp30) cc_final: 0.7700 (tp30)
REVERT: B   14 LEU cc_start: 0.9142 (mm) cc_final: 0.8928 (mm)
REVERT: B   17 GLN cc_start: 0.8363 (pt0) cc_final: 0.7403 (pt0)
REVERT: B   19 GLN cc_start: 0.8226 (tp40) cc_final: 0.7999 (tp40)
REVERT: B   26 MET cc_start: 0.8303 (mtp) cc_final: 0.7706 (mtp)
REVERT: B   30 ASP cc_start: 0.8119 (m-30) cc_final: 0.7675 (m-30)
REVERT: B   33 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8245 (ttp-170)
REVERT: B   37 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7809 (mp0)
REVERT: B   40 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8477 (tm-30)
REVERT: B   42 LYS cc_start: 0.8360 (tptp) cc_final: 0.8076 (tptp)
REVERT: B   74 ARG cc_start: 0.5836 (mmt180) cc_final: 0.4879 (mtm-85)
REVERT: B   80 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7903 (ttp-110)
REVERT: B  131 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7668 (ttp-170)
REVERT: B  142 MET cc_start: 0.7926 (ptt) cc_final: 0.7393 (tmm)
REVERT: B  151 MET cc_start: 0.6344 (tmm) cc_final: 0.4467 (ptm)
REVERT: A   17 ASN cc_start: 0.8694 (m110) cc_final: 0.8424 (m110)
REVERT: A   39 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7663 (ttp-110)
REVERT: A   76 LYS cc_start: 0.9325 (ttpt) cc_final: 0.8957 (tttm)
REVERT: A  119 LYS cc_start: 0.7735 (tptm) cc_final: 0.7488 (mmmt)
REVERT: A  124 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8387 (mm-40)
REVERT: A  128 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7897 (mtm110)
REVERT: A  132 LYS cc_start: 0.8609 (tttt) cc_final: 0.8161 (ttmm)
REVERT: A  142 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7330 (mm-30)
  outliers start: 16
  outliers final: 7
  residues processed: 202
  average time/residue: 0.1030
  time to fit residues: 22.9335
Evaluate side-chains
  206 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 198
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  108 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0470
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
B  18 ASN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.113246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.103829 restraints weight = 6045.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.105782 restraints weight = 3097.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.107144 restraints weight = 1885.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.108021 restraints weight = 1286.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.108335 restraints weight = 959.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.5272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2479  Z= 0.145
  Angle     :  0.715  10.371   3287  Z= 0.356
  Chirality :  0.043   0.180    370
  Planarity :  0.003   0.027    423
  Dihedral  :  3.749  22.306    332
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 30.88 %
    Favored  : 64.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.39 (0.48), residues: 302
  helix:  2.58 (0.30), residues: 275
  sheet:  None (None), residues: 0
  loop : -1.74 (1.40), residues: 27

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 167 
 TYR   0.006   0.001   TYR B  72 
 PHE   0.004   0.001   PHE B  76 
 TRP   0.012   0.002   TRP A  19 
 HIS   0.001   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 2479)
  covalent geometry    : angle       0.71529 ( 3287)
  hydrogen bonds       : bond        0.04798 (  237)
  hydrogen bonds       : angle       3.76142 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 203
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8141 (tp30) cc_final: 0.7653 (tp30)
REVERT: B   14 LEU cc_start: 0.9113 (mm) cc_final: 0.8888 (mm)
REVERT: B   17 GLN cc_start: 0.8345 (pt0) cc_final: 0.7303 (pt0)
REVERT: B   26 MET cc_start: 0.8198 (mtp) cc_final: 0.7623 (mtp)
REVERT: B   30 ASP cc_start: 0.8088 (m-30) cc_final: 0.7585 (m-30)
REVERT: B   31 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7391 (mtt-85)
REVERT: B   33 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8245 (ttp-170)
REVERT: B   37 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7758 (mp0)
REVERT: B   42 LYS cc_start: 0.8405 (tptp) cc_final: 0.8150 (tptp)
REVERT: B   53 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8421 (mp10)
REVERT: B   74 ARG cc_start: 0.5791 (mmt180) cc_final: 0.4784 (mtm-85)
REVERT: B   80 ARG cc_start: 0.8154 (ttt-90) cc_final: 0.7938 (ttp-110)
REVERT: B  131 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7630 (ttp-170)
REVERT: A   17 ASN cc_start: 0.8666 (m110) cc_final: 0.8375 (m110)
REVERT: A   57 LYS cc_start: 0.8698 (pttt) cc_final: 0.8255 (mmtt)
REVERT: A   76 LYS cc_start: 0.9323 (ttpt) cc_final: 0.8950 (tttm)
REVERT: A  119 LYS cc_start: 0.7788 (tptm) cc_final: 0.7533 (mmmt)
REVERT: A  124 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8274 (mm-40)
REVERT: A  127 MET cc_start: 0.7466 (mmp) cc_final: 0.7234 (mmt)
REVERT: A  128 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7794 (mtm110)
REVERT: A  132 LYS cc_start: 0.8644 (tttt) cc_final: 0.8288 (ttmm)
REVERT: A  142 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7338 (mm-30)
REVERT: A  159 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8092 (mm-30)
REVERT: A  162 GLU cc_start: 0.6992 (pm20) cc_final: 0.6322 (tt0)
  outliers start: 13
  outliers final: 9
  residues processed: 205
  average time/residue: 0.1027
  time to fit residues: 23.1005
Evaluate side-chains
  207 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 196
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   53 GLN
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   38 GLN
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  108 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   chunk 0 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  18 ASN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.112673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.103312 restraints weight = 6036.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.105130 restraints weight = 3098.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.106504 restraints weight = 1923.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.107372 restraints weight = 1312.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.107807 restraints weight = 979.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.5439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2479  Z= 0.158
  Angle     :  0.743  10.343   3287  Z= 0.370
  Chirality :  0.043   0.182    370
  Planarity :  0.003   0.027    423
  Dihedral  :  3.784  21.966    332
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 30.88 %
    Favored  : 64.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.32 (0.48), residues: 302
  helix:  2.55 (0.30), residues: 275
  sheet:  None (None), residues: 0
  loop : -1.99 (1.35), residues: 27

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 167 
 TYR   0.007   0.001   TYR B  72 
 PHE   0.004   0.001   PHE B  76 
 TRP   0.011   0.002   TRP A  19 
 HIS   0.001   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 2479)
  covalent geometry    : angle       0.74326 ( 3287)
  hydrogen bonds       : bond        0.04812 (  237)
  hydrogen bonds       : angle       3.81394 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 201
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8144 (tp30) cc_final: 0.7682 (tp30)
REVERT: B   14 LEU cc_start: 0.9109 (mm) cc_final: 0.8904 (mm)
REVERT: B   17 GLN cc_start: 0.8342 (pt0) cc_final: 0.7324 (pt0)
REVERT: B   26 MET cc_start: 0.8156 (mtp) cc_final: 0.7574 (mtp)
REVERT: B   30 ASP cc_start: 0.8064 (m-30) cc_final: 0.7557 (m-30)
REVERT: B   31 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7413 (mtt-85)
REVERT: B   33 ARG cc_start: 0.8768 (ttp80) cc_final: 0.8254 (ttp-170)
REVERT: B   37 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7796 (mp0)
REVERT: B   42 LYS cc_start: 0.8322 (tptp) cc_final: 0.7909 (tptp)
REVERT: B   46 ASP cc_start: 0.7531 (m-30) cc_final: 0.6595 (m-30)
REVERT: B   74 ARG cc_start: 0.5793 (mmt180) cc_final: 0.4765 (mtm-85)
REVERT: B   80 ARG cc_start: 0.8171 (ttt-90) cc_final: 0.7962 (ttp-110)
REVERT: B  131 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7676 (ttp-170)
REVERT: A   17 ASN cc_start: 0.8697 (m110) cc_final: 0.8381 (m110)
REVERT: A   39 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7700 (mtm-85)
REVERT: A   57 LYS cc_start: 0.8628 (pttt) cc_final: 0.8177 (mmtt)
REVERT: A   76 LYS cc_start: 0.9339 (ttpt) cc_final: 0.8963 (tttm)
REVERT: A  112 LYS cc_start: 0.8815 (tppt) cc_final: 0.8542 (tppt)
REVERT: A  119 LYS cc_start: 0.7819 (tptm) cc_final: 0.7571 (mmmt)
REVERT: A  124 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8492 (mm-40)
REVERT: A  128 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7805 (mtm110)
REVERT: A  132 LYS cc_start: 0.8631 (tttt) cc_final: 0.8325 (ttmm)
REVERT: A  142 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7341 (mm-30)
REVERT: A  160 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7914 (mt-10)
  outliers start: 12
  outliers final: 10
  residues processed: 202
  average time/residue: 0.0944
  time to fit residues: 20.8548
Evaluate side-chains
  209 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 198
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   38 GLN
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  108 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.112598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.103066 restraints weight = 6047.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.104990 restraints weight = 3096.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.106357 restraints weight = 1893.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.107016 restraints weight = 1299.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.107724 restraints weight = 1019.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.5631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   2479  Z= 0.175
  Angle     :  0.772   9.779   3287  Z= 0.388
  Chirality :  0.044   0.181    370
  Planarity :  0.004   0.028    423
  Dihedral  :  3.796  21.146    332
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 29.41 %
    Favored  : 65.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.24 (0.48), residues: 302
  helix:  2.51 (0.30), residues: 275
  sheet:  None (None), residues: 0
  loop : -2.17 (1.30), residues: 27

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 167 
 TYR   0.008   0.001   TYR B  72 
 PHE   0.005   0.001   PHE B 129 
 TRP   0.011   0.003   TRP A  19 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 2479)
  covalent geometry    : angle       0.77174 ( 3287)
  hydrogen bonds       : bond        0.04850 (  237)
  hydrogen bonds       : angle       3.86812 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8104 (tp30) cc_final: 0.7645 (tp30)
REVERT: B   14 LEU cc_start: 0.9118 (mm) cc_final: 0.8915 (mm)
REVERT: B   17 GLN cc_start: 0.8345 (pt0) cc_final: 0.7306 (pt0)
REVERT: B   26 MET cc_start: 0.8183 (mtp) cc_final: 0.7590 (mtp)
REVERT: B   30 ASP cc_start: 0.8096 (m-30) cc_final: 0.7375 (m-30)
REVERT: B   31 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7383 (mtt-85)
REVERT: B   33 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8280 (ttp-170)
REVERT: B   37 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7830 (mp0)
REVERT: B   42 LYS cc_start: 0.8316 (tptp) cc_final: 0.7925 (tptp)
REVERT: B   46 ASP cc_start: 0.7558 (m-30) cc_final: 0.6597 (m-30)
REVERT: B   74 ARG cc_start: 0.5691 (mmt180) cc_final: 0.4298 (mtt-85)
REVERT: B   80 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.7977 (ttp-170)
REVERT: B  131 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7697 (ttp-170)
REVERT: A   17 ASN cc_start: 0.8696 (m110) cc_final: 0.8380 (m110)
REVERT: A   39 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7653 (mtm-85)
REVERT: A   57 LYS cc_start: 0.8550 (pttt) cc_final: 0.8213 (mmtt)
REVERT: A   76 LYS cc_start: 0.9358 (ttpt) cc_final: 0.8972 (tttm)
REVERT: A  112 LYS cc_start: 0.8808 (tppt) cc_final: 0.8576 (tppt)
REVERT: A  119 LYS cc_start: 0.7846 (tptm) cc_final: 0.7608 (mmmt)
REVERT: A  132 LYS cc_start: 0.8677 (tttt) cc_final: 0.8328 (ttmm)
REVERT: A  142 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7400 (mm-30)
  outliers start: 15
  outliers final: 11
  residues processed: 201
  average time/residue: 0.0908
  time to fit residues: 20.0520
Evaluate side-chains
  209 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 197
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   38 GLN
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  126 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0470
   chunk 25 optimal weight:    0.4980
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    0.4980
   chunk 13 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
B  18 ASN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.113538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.104112 restraints weight = 6110.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.106073 restraints weight = 3058.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.107476 restraints weight = 1847.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.108365 restraints weight = 1256.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.108789 restraints weight = 937.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2479  Z= 0.156
  Angle     :  0.762  10.913   3287  Z= 0.378
  Chirality :  0.043   0.187    370
  Planarity :  0.003   0.028    423
  Dihedral  :  3.765  21.240    332
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 31.99 %
    Favored  : 63.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.22 (0.48), residues: 302
  helix:  2.50 (0.30), residues: 275
  sheet:  None (None), residues: 0
  loop : -2.14 (1.30), residues: 27

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 167 
 TYR   0.008   0.001   TYR B  72 
 PHE   0.003   0.001   PHE B  76 
 TRP   0.011   0.002   TRP A  19 
 HIS   0.001   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 2479)
  covalent geometry    : angle       0.76245 ( 3287)
  hydrogen bonds       : bond        0.04755 (  237)
  hydrogen bonds       : angle       3.82397 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 201
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8151 (tp30) cc_final: 0.7560 (tp30)
REVERT: B   14 LEU cc_start: 0.9067 (mm) cc_final: 0.8852 (mm)
REVERT: B   17 GLN cc_start: 0.8392 (pt0) cc_final: 0.7222 (pt0)
REVERT: B   20 ARG cc_start: 0.7467 (ptt180) cc_final: 0.7143 (ptt180)
REVERT: B   26 MET cc_start: 0.8129 (mtp) cc_final: 0.7528 (mtp)
REVERT: B   30 ASP cc_start: 0.8128 (m-30) cc_final: 0.7575 (m-30)
REVERT: B   31 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.7409 (mtt-85)
REVERT: B   33 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8268 (ttp-170)
REVERT: B   37 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7752 (mp0)
REVERT: B   42 LYS cc_start: 0.8332 (tptp) cc_final: 0.8055 (tptp)
REVERT: B   53 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8495 (mp10)
REVERT: B   74 ARG cc_start: 0.5622 (mmt180) cc_final: 0.4294 (mtt90)
REVERT: B   80 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.7990 (ttp-110)
REVERT: B  123 GLN cc_start: 0.8132 (tt0) cc_final: 0.7896 (tt0)
REVERT: B  131 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7711 (ttp-170)
REVERT: B  151 MET cc_start: 0.6277 (tmm) cc_final: 0.5369 (tmm)
REVERT: A   17 ASN cc_start: 0.8694 (m110) cc_final: 0.8383 (m110)
REVERT: A   57 LYS cc_start: 0.8586 (pttt) cc_final: 0.8221 (mmtt)
REVERT: A   76 LYS cc_start: 0.9362 (ttpt) cc_final: 0.8989 (tttm)
REVERT: A  112 LYS cc_start: 0.8858 (tppt) cc_final: 0.8602 (tppt)
REVERT: A  128 ARG cc_start: 0.8190 (mtm110) cc_final: 0.7777 (mtm110)
REVERT: A  132 LYS cc_start: 0.8652 (tttt) cc_final: 0.8330 (ttmm)
REVERT: A  142 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7357 (mm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 203
  average time/residue: 0.0939
  time to fit residues: 20.8775
Evaluate side-chains
  209 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 197
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   53 GLN
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   38 GLN
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  126 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0770
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0040
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.4150

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

Flipped N/Q/H residues before XYZ refinement:
B  18 ASN
A  38 GLN
A 124 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.113847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.104224 restraints weight = 6171.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.106279 restraints weight = 3091.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.107718 restraints weight = 1848.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.108650 restraints weight = 1247.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.109140 restraints weight = 929.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.5742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2479  Z= 0.157
  Angle     :  0.789  10.814   3287  Z= 0.391
  Chirality :  0.043   0.184    370
  Planarity :  0.004   0.027    423
  Dihedral  :  3.724  20.884    332
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 31.99 %
    Favored  : 63.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.22 (0.48), residues: 302
  helix:  2.47 (0.30), residues: 276
  sheet:  None (None), residues: 0
  loop : -1.95 (1.34), residues: 26

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 167 
 TYR   0.008   0.001   TYR B  72 
 PHE   0.003   0.001   PHE B  76 
 TRP   0.009   0.002   TRP A  19 
 HIS   0.001   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 2479)
  covalent geometry    : angle       0.78866 ( 3287)
  hydrogen bonds       : bond        0.04736 (  237)
  hydrogen bonds       : angle       3.82758 (  711)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 199
  time to evaluate  : 0.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8145 (tp30) cc_final: 0.7571 (tp30)
REVERT: B   14 LEU cc_start: 0.9065 (mm) cc_final: 0.8859 (mm)
REVERT: B   17 GLN cc_start: 0.8445 (pt0) cc_final: 0.7295 (pt0)
REVERT: B   20 ARG cc_start: 0.7476 (ptt180) cc_final: 0.7182 (ptt180)
REVERT: B   30 ASP cc_start: 0.8148 (m-30) cc_final: 0.7646 (m-30)
REVERT: B   31 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.7411 (mtt-85)
REVERT: B   33 ARG cc_start: 0.8764 (ttp80) cc_final: 0.8327 (ttp-170)
REVERT: B   37 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7727 (mp0)
REVERT: B   42 LYS cc_start: 0.8325 (tptp) cc_final: 0.8048 (tptp)
REVERT: B   74 ARG cc_start: 0.5589 (mmt180) cc_final: 0.4270 (mtt90)
REVERT: B  123 GLN cc_start: 0.8190 (tt0) cc_final: 0.7953 (tt0)
REVERT: B  131 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7710 (ttp-170)
REVERT: B  151 MET cc_start: 0.6307 (tmm) cc_final: 0.5399 (tmm)
REVERT: A   17 ASN cc_start: 0.8699 (m110) cc_final: 0.8388 (m110)
REVERT: A   57 LYS cc_start: 0.8640 (pttt) cc_final: 0.8280 (mmtt)
REVERT: A   76 LYS cc_start: 0.9363 (ttpt) cc_final: 0.8988 (tttm)
REVERT: A  112 LYS cc_start: 0.8857 (tppt) cc_final: 0.8626 (tppt)
REVERT: A  132 LYS cc_start: 0.8655 (tttt) cc_final: 0.8335 (ttmm)
REVERT: A  142 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7350 (mm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 201
  average time/residue: 0.0985
  time to fit residues: 21.6778
Evaluate side-chains
  205 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 194
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   38 GLN
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  126 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  38 GLN
A 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.113423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.103853 restraints weight = 6180.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.105859 restraints weight = 3096.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.107267 restraints weight = 1864.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.108104 restraints weight = 1261.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.108745 restraints weight = 953.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.5824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2479  Z= 0.169
  Angle     :  0.790  10.497   3287  Z= 0.398
  Chirality :  0.044   0.185    370
  Planarity :  0.004   0.029    423
  Dihedral  :  3.716  20.087    332
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 32.72 %
    Favored  : 63.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.22 (0.48), residues: 302
  helix:  2.45 (0.30), residues: 277
  sheet:  None (None), residues: 0
  loop : -1.91 (1.41), residues: 25

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 167 
 TYR   0.007   0.001   TYR B  72 
 PHE   0.003   0.001   PHE B  76 
 TRP   0.010   0.002   TRP A  19 
 HIS   0.001   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 2479)
  covalent geometry    : angle       0.78978 ( 3287)
  hydrogen bonds       : bond        0.04736 (  237)
  hydrogen bonds       : angle       3.87017 (  711)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1411.21 seconds
wall clock time: 25 minutes 2.31 seconds (1502.31 seconds total)