Starting phenix.real_space_refine
on Tue Feb  3 15:58:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mja_48313/02_2026/9mja_48313.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mja_48313/02_2026/9mja_48313.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mja_48313/02_2026/9mja_48313.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mja_48313/02_2026/9mja_48313.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mja_48313/02_2026/9mja_48313.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mja_48313/02_2026/9mja_48313.cif"
  }
  resolution = 4.3
  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=   0.023
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      17      5.16       5
     C    2904      2.51       5
     N     766      2.21       5
     O     848      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4535
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1935
          Classifications: {'peptide': 244}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 231}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2561
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 13, 'TRANS': 302}
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 39
          Unusual residues: {'UHB': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.97, per 1000 atoms: 0.21
  Number of scatterers: 4535
  At special positions: 0
  Unit cell: (64.672, 70.688, 115.808, 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      17     16.00
     O     848      8.00
     N     766      7.00
     C    2904      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: 0.23
  Conformation dependent library (CDL) restraints added in 335.6 milliseconds
  

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1050

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 5 sheets defined
      45.0% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 666 through 677
    Processing helix  chain 'A' and resid 789 through 797
    Processing helix  chain 'A' and resid 808 through 821
    Processing helix  chain 'A' and resid 843 through 849
    Processing helix  chain 'A' and resid 850 through 852
      No H-bonds generated for 'chain 'A' and resid 850 through 852'
    Processing helix  chain 'A' and resid 865 through 867
      No H-bonds generated for 'chain 'A' and resid 865 through 867'
    Processing helix  chain 'A' and resid 868 through 876
    Processing helix  chain 'A' and resid 885 through 889
      removed outlier: 3.649A  pdb=" N   TYR A 889 " --> pdb=" O   VAL A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 906
    Processing helix  chain 'A' and resid 907 through 909
      No H-bonds generated for 'chain 'A' and resid 907 through 909'
    Processing helix  chain 'B' and resid 34 through 45
    Processing helix  chain 'B' and resid 50 through 64
      removed outlier: 4.022A  pdb=" N   TYR B  54 " --> pdb=" O   PRO B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 77
    Processing helix  chain 'B' and resid 82 through 88
    Processing helix  chain 'B' and resid 160 through 176
    Processing helix  chain 'B' and resid 178 through 200
    Processing helix  chain 'B' and resid 207 through 216
      removed outlier: 3.944A  pdb=" N   LYS B 216 " --> pdb=" O   GLN B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 258
    Processing helix  chain 'B' and resid 260 through 268
    Processing helix  chain 'B' and resid 268 through 284
    Processing helix  chain 'B' and resid 286 through 301
      removed outlier: 4.210A  pdb=" N   GLY B 290 " --> pdb=" O   ASP B 286 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLY B 301 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 304
      No H-bonds generated for 'chain 'B' and resid 302 through 304'
    Processing helix  chain 'B' and resid 305 through 320
      Proline residue:  B 314  - end of helix
    Processing helix  chain 'B' and resid 322 through 335
    Processing sheet with id=AA1, first strand: chain 'A' and resid 799 through 803
      removed outlier: 4.038A  pdb=" N   ASP A 800 " --> pdb=" O   GLU A 840 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   LEU A 831 " --> pdb=" O   ASN A1008 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   ASN A1008 " --> pdb=" O   LEU A 831 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   VAL A 833 " --> pdb=" O   LYS A1006 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   LYS A1006 " --> pdb=" O   VAL A 833 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ASP A 835 " --> pdb=" O   LYS A1004 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS A1004 " --> pdb=" O   ASP A 835 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   LYS A1000 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   ARG A 841 " --> pdb=" O   ASN A 998 " (cutoff:3.500A)
      removed outlier: 9.025A  pdb=" N   ASN A 998 " --> pdb=" O   ARG A 841 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   LEU A 999 " --> pdb=" O   GLU A 923 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   GLU A 923 " --> pdb=" O   LEU A 999 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 895 through 897
      removed outlier: 3.773A  pdb=" N   VAL A 991 " --> pdb=" O   ILE A 895 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   TYR A 930 " --> pdb=" O   LYS A 949 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 954 through 955
      removed outlier: 3.545A  pdb=" N   ILE A 975 " --> pdb=" O   THR A 955 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 962 through 964
      removed outlier: 3.515A  pdb=" N   ILE A 962 " --> pdb=" O   VAL A 969 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 80
      removed outlier: 3.681A  pdb=" N   GLN B  79 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE B 120 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   THR B 117 " --> pdb=" O   TYR B 131 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   TYR B 131 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   HIS B 128 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   TYR B 142 " --> pdb=" O   PHE B 132 " (cutoff:3.500A)

    188 hydrogen bonds defined for protein.
    549 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: 0.66

  Time building geometry restraints manager: 0.32 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1209
        1.33 -     1.45: 820
        1.45 -     1.57: 2582
        1.57 -     1.69: 0
        1.69 -     1.81: 27
  Bond restraints: 4638
  Sorted by residual:
  bond pdb=" CG1 ILE A 872 "
       pdb=" CD1 ILE A 872 "
    ideal  model  delta    sigma   weight residual
    1.513  1.478  0.035 3.90e-02 6.57e+02 7.96e-01
  bond pdb=" N   GLY B  99 "
       pdb=" CA  GLY B  99 "
    ideal  model  delta    sigma   weight residual
    1.453  1.442  0.011 1.47e-02 4.63e+03 6.04e-01
  bond pdb=" CA  ASP A 981 "
       pdb=" CB  ASP A 981 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.013 1.69e-02 3.50e+03 5.96e-01
  bond pdb=" N   THR B  93 "
       pdb=" CA  THR B  93 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.29e-02 6.01e+03 5.87e-01
  bond pdb=" CB  MET B 274 "
       pdb=" CG  MET B 274 "
    ideal  model  delta    sigma   weight residual
    1.520  1.499  0.021 3.00e-02 1.11e+03 4.97e-01
  ... (remaining 4633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 6027
        1.38 -     2.76: 198
        2.76 -     4.15: 31
        4.15 -     5.53: 9
        5.53 -     6.91: 1
  Bond angle restraints: 6266
  Sorted by residual:
  angle pdb=" N   ILE B 341 "
        pdb=" CA  ILE B 341 "
        pdb=" C   ILE B 341 "
      ideal   model   delta    sigma   weight residual
     113.20  110.05    3.15 9.60e-01 1.09e+00 1.07e+01
  angle pdb=" N   LYS B  90 "
        pdb=" CA  LYS B  90 "
        pdb=" C   LYS B  90 "
      ideal   model   delta    sigma   weight residual
     113.18  109.73    3.45 1.21e+00 6.83e-01 8.14e+00
  angle pdb=" C   ASN A 980 "
        pdb=" N   ASP A 981 "
        pdb=" CA  ASP A 981 "
      ideal   model   delta    sigma   weight residual
     121.54  126.93   -5.39 1.91e+00 2.74e-01 7.97e+00
  angle pdb=" N   SER A 864 "
        pdb=" CA  SER A 864 "
        pdb=" C   SER A 864 "
      ideal   model   delta    sigma   weight residual
     108.60  112.56   -3.96 1.46e+00 4.69e-01 7.35e+00
  angle pdb=" N   LYS B  92 "
        pdb=" CA  LYS B  92 "
        pdb=" C   LYS B  92 "
      ideal   model   delta    sigma   weight residual
     108.24  111.57   -3.33 1.32e+00 5.74e-01 6.37e+00
  ... (remaining 6261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.46: 2408
       14.46 -    28.91: 306
       28.91 -    43.37: 73
       43.37 -    57.82: 21
       57.82 -    72.28: 9
  Dihedral angle restraints: 2817
    sinusoidal: 1184
      harmonic: 1633
  Sorted by residual:
  dihedral pdb=" CA  ASP A 671 "
           pdb=" CB  ASP A 671 "
           pdb=" CG  ASP A 671 "
           pdb=" OD1 ASP A 671 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.45   57.45     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  ASP B 235 "
           pdb=" CB  ASP B 235 "
           pdb=" CG  ASP B 235 "
           pdb=" OD1 ASP B 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.33   52.33     1      2.00e+01 2.50e-03 9.33e+00
  dihedral pdb=" CA  ASP A 835 "
           pdb=" CB  ASP A 835 "
           pdb=" CG  ASP A 835 "
           pdb=" OD1 ASP A 835 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.76   51.76     1      2.00e+01 2.50e-03 9.15e+00
  ... (remaining 2814 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 366
       0.027 -    0.054: 197
       0.054 -    0.080: 66
       0.080 -    0.107: 38
       0.107 -    0.134: 15
  Chirality restraints: 682
  Sorted by residual:
  chirality pdb=" CA  LEU B 313 "
            pdb=" N   LEU B 313 "
            pdb=" C   LEU B 313 "
            pdb=" CB  LEU B 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  ASP A 981 "
            pdb=" N   ASP A 981 "
            pdb=" C   ASP A 981 "
            pdb=" CB  ASP A 981 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.44e-01
  chirality pdb=" CA  ILE A 990 "
            pdb=" N   ILE A 990 "
            pdb=" C   ILE A 990 "
            pdb=" CB  ILE A 990 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 679 not shown)

  Planarity restraints: 801
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 884 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.28e+00
        pdb=" N   PRO A 885 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 885 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 885 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 955 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.44e+00
        pdb=" N   PRO A 956 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 956 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 956 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 788 "   -0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO A 789 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 789 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 789 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 798 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 432
        2.74 -     3.28: 4612
        3.28 -     3.82: 7509
        3.82 -     4.36: 8307
        4.36 -     4.90: 14121
  Nonbonded interactions: 34981
  Sorted by model distance:
  nonbonded pdb=" O   TRP B 106 "
            pdb=" OG1 THR B 117 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OE1 GLN B 116 "
            pdb=" NH2 ARG B 133 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" ND2 ASN A 820 "
            pdb=" O   LEU A 971 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" N   GLU A 809 "
            pdb=" OE1 GLU A 809 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OG  SER B 260 "
            pdb=" OE1 GLU B 263 "
     model   vdw
     2.288 3.040
  ... (remaining 34976 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=0.00 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:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
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      :  0.003   0.035   4638  Z= 0.132
  Angle     :  0.605   6.910   6266  Z= 0.336
  Chirality :  0.042   0.134    682
  Planarity :  0.004   0.057    801
  Dihedral  : 14.380  72.278   1767
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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: -0.20 (0.35), residues: 554
  helix:  0.68 (0.34), residues: 229
  sheet: -0.67 (0.78), residues: 49
  loop : -0.66 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 865 
 TYR   0.013   0.001   TYR B 238 
 PHE   0.014   0.001   PHE A 869 
 TRP   0.015   0.002   TRP A1014 
 HIS   0.003   0.001   HIS A 855 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4638)
  covalent geometry    : angle       0.60455 ( 6266)
  hydrogen bonds       : bond        0.16121 (  188)
  hydrogen bonds       : angle       6.53393 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  963 SER cc_start: 0.7201 (t) cc_final: 0.6947 (m)
REVERT: B  274 MET cc_start: 0.7627 (mmt) cc_final: 0.7363 (mmm)
REVERT: B  308 VAL cc_start: 0.8796 (t) cc_final: 0.8560 (p)
REVERT: B  328 ILE cc_start: 0.8786 (mm) cc_final: 0.8223 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0670
  time to fit residues: 10.5225
Evaluate side-chains
  57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.2980
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 820 ASN
A 855 HIS
A 868 ASN
A 987 ASN
B  44 HIS
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.061790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.050054 restraints weight = 23879.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.051941 restraints weight = 14688.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.053425 restraints weight = 10192.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.054541 restraints weight = 7605.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.055398 restraints weight = 5987.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4638  Z= 0.122
  Angle     :  0.592   6.896   6266  Z= 0.302
  Chirality :  0.044   0.196    682
  Planarity :  0.005   0.058    801
  Dihedral  :  5.314  37.068    636
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  2.84 %
    Favored  : 96.75 %
  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:  0.04 (0.36), residues: 554
  helix:  0.82 (0.35), residues: 230
  sheet: -0.30 (0.69), residues: 68
  loop : -0.53 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 213 
 TYR   0.019   0.002   TYR A 989 
 PHE   0.016   0.001   PHE A 897 
 TRP   0.010   0.002   TRP A1014 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 4638)
  covalent geometry    : angle       0.59217 ( 6266)
  hydrogen bonds       : bond        0.03796 (  188)
  hydrogen bonds       : angle       5.38390 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.9504 (mt0) cc_final: 0.9191 (mt0)
REVERT: A  791 ASP cc_start: 0.8974 (t0) cc_final: 0.8569 (t0)
REVERT: A  821 THR cc_start: 0.8034 (t) cc_final: 0.7623 (t)
REVERT: A  837 PHE cc_start: 0.7739 (m-80) cc_final: 0.7197 (m-10)
REVERT: A  903 LYS cc_start: 0.9497 (tppp) cc_final: 0.9018 (tppt)
REVERT: B  274 MET cc_start: 0.9168 (mmt) cc_final: 0.8723 (mmm)
REVERT: B  327 GLU cc_start: 0.9508 (pt0) cc_final: 0.9120 (pp20)
  outliers start: 2
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0655
  time to fit residues: 7.0388
Evaluate side-chains
  56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 934 HIS
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.056727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.045430 restraints weight = 24367.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.047382 restraints weight = 14225.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.048810 restraints weight = 9590.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.049889 restraints weight = 7044.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.050587 restraints weight = 5514.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4638  Z= 0.165
  Angle     :  0.609   6.976   6266  Z= 0.308
  Chirality :  0.043   0.164    682
  Planarity :  0.004   0.057    801
  Dihedral  :  5.337  36.162    636
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.46 %
    Favored  : 95.33 %
  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:  0.11 (0.36), residues: 554
  helix:  0.94 (0.35), residues: 230
  sheet:  0.10 (0.70), residues: 62
  loop : -0.66 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 858 
 TYR   0.015   0.002   TYR B  45 
 PHE   0.021   0.002   PHE A 897 
 TRP   0.009   0.002   TRP A1014 
 HIS   0.005   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4638)
  covalent geometry    : angle       0.60851 ( 6266)
  hydrogen bonds       : bond        0.03742 (  188)
  hydrogen bonds       : angle       5.49639 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.9457 (mt0) cc_final: 0.9150 (mt0)
REVERT: A  791 ASP cc_start: 0.8932 (t0) cc_final: 0.8669 (t0)
REVERT: A  837 PHE cc_start: 0.7832 (m-80) cc_final: 0.7406 (m-10)
REVERT: A  903 LYS cc_start: 0.9562 (tppp) cc_final: 0.9055 (tppt)
REVERT: B  271 ILE cc_start: 0.9382 (pt) cc_final: 0.9138 (pt)
REVERT: B  274 MET cc_start: 0.9275 (mmt) cc_final: 0.8833 (mmm)
REVERT: B  289 MET cc_start: 0.8813 (tmm) cc_final: 0.8362 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0584
  time to fit residues: 5.5951
Evaluate side-chains
  47 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 18 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** B 103 ASN ** 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 = 0.3200 r_free = 0.3200 target = 0.057199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.045906 restraints weight = 24283.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.047868 restraints weight = 14112.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.049251 restraints weight = 9471.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.050395 restraints weight = 6964.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.051185 restraints weight = 5431.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4638  Z= 0.137
  Angle     :  0.569   6.123   6266  Z= 0.289
  Chirality :  0.042   0.155    682
  Planarity :  0.004   0.058    801
  Dihedral  :  5.265  34.652    636
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.36), residues: 554
  helix:  1.01 (0.36), residues: 229
  sheet:  0.10 (0.67), residues: 64
  loop : -0.71 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 322 
 TYR   0.015   0.001   TYR A 889 
 PHE   0.017   0.002   PHE A 897 
 TRP   0.006   0.001   TRP A 861 
 HIS   0.002   0.001   HIS B  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4638)
  covalent geometry    : angle       0.56851 ( 6266)
  hydrogen bonds       : bond        0.03536 (  188)
  hydrogen bonds       : angle       5.32457 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.9453 (mt0) cc_final: 0.9152 (mt0)
REVERT: A  791 ASP cc_start: 0.9097 (t0) cc_final: 0.8548 (t70)
REVERT: A  821 THR cc_start: 0.8126 (t) cc_final: 0.7893 (t)
REVERT: A  837 PHE cc_start: 0.7667 (m-80) cc_final: 0.7328 (m-10)
REVERT: A  903 LYS cc_start: 0.9548 (tppp) cc_final: 0.8956 (tppt)
REVERT: B   60 CYS cc_start: 0.9629 (m) cc_final: 0.9423 (m)
REVERT: B  271 ILE cc_start: 0.9375 (pt) cc_final: 0.9162 (pt)
REVERT: B  274 MET cc_start: 0.9270 (mmt) cc_final: 0.8831 (mmm)
REVERT: B  289 MET cc_start: 0.8884 (tmm) cc_final: 0.8402 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0461
  time to fit residues: 4.2994
Evaluate side-chains
  44 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0770
   chunk 39 optimal weight:    0.5980
   chunk 18 optimal weight:    8.9990
   overall best weight:    0.6742

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

Flipped N/Q/H residues before XYZ refinement:
** A 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 HIS
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.058096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.046929 restraints weight = 23565.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.048964 restraints weight = 13480.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.050514 restraints weight = 8939.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.051619 restraints weight = 6462.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.052460 restraints weight = 4977.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4638  Z= 0.114
  Angle     :  0.555   7.958   6266  Z= 0.279
  Chirality :  0.042   0.186    682
  Planarity :  0.004   0.055    801
  Dihedral  :  5.182  35.447    636
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  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:  0.06 (0.36), residues: 554
  helix:  1.01 (0.36), residues: 229
  sheet: -0.27 (0.67), residues: 64
  loop : -0.72 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 857 
 TYR   0.014   0.001   TYR A 889 
 PHE   0.010   0.001   PHE A 891 
 TRP   0.007   0.001   TRP A 861 
 HIS   0.003   0.001   HIS B  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4638)
  covalent geometry    : angle       0.55520 ( 6266)
  hydrogen bonds       : bond        0.03385 (  188)
  hydrogen bonds       : angle       5.19217 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.9427 (mt0) cc_final: 0.9104 (mt0)
REVERT: A  791 ASP cc_start: 0.8890 (t0) cc_final: 0.8511 (t70)
REVERT: A  792 VAL cc_start: 0.9449 (t) cc_final: 0.9214 (t)
REVERT: A  837 PHE cc_start: 0.7602 (m-80) cc_final: 0.7148 (m-80)
REVERT: A  840 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8078 (mp0)
REVERT: A  869 PHE cc_start: 0.8539 (m-80) cc_final: 0.8027 (m-10)
REVERT: B  271 ILE cc_start: 0.9307 (pt) cc_final: 0.9104 (pt)
REVERT: B  274 MET cc_start: 0.9239 (mmt) cc_final: 0.8783 (mmm)
REVERT: B  327 GLU cc_start: 0.9605 (pt0) cc_final: 0.9220 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0494
  time to fit residues: 4.4167
Evaluate side-chains
  45 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 HIS ** 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 = 0.3146 r_free = 0.3146 target = 0.054271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.043387 restraints weight = 25162.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.045324 restraints weight = 14365.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.046687 restraints weight = 9553.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.047792 restraints weight = 6983.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.048451 restraints weight = 5414.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.4327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4638  Z= 0.211
  Angle     :  0.641   6.163   6266  Z= 0.328
  Chirality :  0.043   0.175    682
  Planarity :  0.004   0.055    801
  Dihedral  :  5.464  33.334    636
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  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: -0.11 (0.35), residues: 554
  helix:  0.81 (0.36), residues: 222
  sheet: -0.50 (0.65), residues: 65
  loop : -0.66 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 322 
 TYR   0.016   0.002   TYR B  45 
 PHE   0.017   0.002   PHE A 897 
 TRP   0.009   0.002   TRP B  57 
 HIS   0.005   0.001   HIS A 862 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 4638)
  covalent geometry    : angle       0.64052 ( 6266)
  hydrogen bonds       : bond        0.03852 (  188)
  hydrogen bonds       : angle       5.61944 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  791 ASP cc_start: 0.8952 (t0) cc_final: 0.8617 (t70)
REVERT: A  837 PHE cc_start: 0.7862 (m-80) cc_final: 0.7375 (m-80)
REVERT: A  840 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8011 (mp0)
REVERT: A  912 GLN cc_start: 0.9598 (tm-30) cc_final: 0.9250 (mm-40)
REVERT: A  988 GLU cc_start: 0.9373 (mt-10) cc_final: 0.9069 (mp0)
REVERT: B   56 PHE cc_start: 0.9525 (t80) cc_final: 0.8893 (t80)
REVERT: B   60 CYS cc_start: 0.9613 (m) cc_final: 0.9279 (m)
REVERT: B  274 MET cc_start: 0.9311 (mmt) cc_final: 0.8815 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0528
  time to fit residues: 4.5845
Evaluate side-chains
  43 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0980
   chunk 15 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 HIS
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.054640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.043682 restraints weight = 25521.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.045611 restraints weight = 14636.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.047058 restraints weight = 9792.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.048136 restraints weight = 7133.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.048931 restraints weight = 5537.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.4517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4638  Z= 0.169
  Angle     :  0.609  10.385   6266  Z= 0.306
  Chirality :  0.043   0.172    682
  Planarity :  0.004   0.056    801
  Dihedral  :  5.401  31.637    636
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  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: -0.08 (0.35), residues: 554
  helix:  0.93 (0.37), residues: 221
  sheet: -0.64 (0.65), residues: 65
  loop : -0.68 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 264 
 TYR   0.013   0.002   TYR B  45 
 PHE   0.010   0.002   PHE A 869 
 TRP   0.006   0.001   TRP A 861 
 HIS   0.004   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4638)
  covalent geometry    : angle       0.60868 ( 6266)
  hydrogen bonds       : bond        0.03669 (  188)
  hydrogen bonds       : angle       5.53785 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  791 ASP cc_start: 0.8922 (t0) cc_final: 0.8523 (t70)
REVERT: A  837 PHE cc_start: 0.7827 (m-80) cc_final: 0.7361 (m-80)
REVERT: A  840 GLU cc_start: 0.9026 (mt-10) cc_final: 0.7985 (mm-30)
REVERT: A  869 PHE cc_start: 0.8741 (m-80) cc_final: 0.8229 (m-10)
REVERT: A  912 GLN cc_start: 0.9591 (tm-30) cc_final: 0.9255 (mm-40)
REVERT: A  946 HIS cc_start: 0.9316 (m170) cc_final: 0.9029 (m90)
REVERT: B   56 PHE cc_start: 0.9517 (t80) cc_final: 0.8836 (t80)
REVERT: B   60 CYS cc_start: 0.9616 (m) cc_final: 0.9270 (m)
REVERT: B  169 LEU cc_start: 0.9528 (tp) cc_final: 0.9118 (pp)
REVERT: B  274 MET cc_start: 0.9373 (mmt) cc_final: 0.8838 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0529
  time to fit residues: 4.6848
Evaluate side-chains
  44 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0170
   chunk 5 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5420

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

Flipped N/Q/H residues before XYZ refinement:
A 793 ASN
B  44 HIS
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 279 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.056416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.045456 restraints weight = 24441.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.047494 restraints weight = 13703.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.048992 restraints weight = 8999.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.050088 restraints weight = 6513.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.050926 restraints weight = 5029.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.4616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4638  Z= 0.110
  Angle     :  0.571   8.558   6266  Z= 0.281
  Chirality :  0.042   0.176    682
  Planarity :  0.004   0.055    801
  Dihedral  :  5.128  32.180    636
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.36), residues: 554
  helix:  0.93 (0.36), residues: 230
  sheet: -0.58 (0.66), residues: 63
  loop : -0.58 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 322 
 TYR   0.015   0.001   TYR B  45 
 PHE   0.015   0.002   PHE A 897 
 TRP   0.005   0.001   TRP A 861 
 HIS   0.008   0.001   HIS B  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 4638)
  covalent geometry    : angle       0.57093 ( 6266)
  hydrogen bonds       : bond        0.03405 (  188)
  hydrogen bonds       : angle       5.28205 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  791 ASP cc_start: 0.9002 (t0) cc_final: 0.8583 (t70)
REVERT: A  837 PHE cc_start: 0.7738 (m-80) cc_final: 0.7331 (m-80)
REVERT: A  840 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8036 (mm-30)
REVERT: A  857 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.7562 (mtp85)
REVERT: A  903 LYS cc_start: 0.9551 (tppp) cc_final: 0.9027 (tppt)
REVERT: A  912 GLN cc_start: 0.9585 (tm-30) cc_final: 0.9360 (mm-40)
REVERT: A  929 MET cc_start: 0.7723 (mtt) cc_final: 0.7129 (mmm)
REVERT: A  946 HIS cc_start: 0.9254 (m170) cc_final: 0.8974 (m90)
REVERT: A 1003 LEU cc_start: 0.9399 (mt) cc_final: 0.9173 (mt)
REVERT: B   56 PHE cc_start: 0.9501 (t80) cc_final: 0.8927 (t80)
REVERT: B   60 CYS cc_start: 0.9592 (m) cc_final: 0.9265 (m)
REVERT: B  169 LEU cc_start: 0.9478 (tp) cc_final: 0.9068 (pp)
REVERT: B  274 MET cc_start: 0.9355 (mmt) cc_final: 0.8831 (mmm)
REVERT: B  327 GLU cc_start: 0.9618 (pt0) cc_final: 0.9227 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0582
  time to fit residues: 5.0296
Evaluate side-chains
  44 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 103 ASN ** 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 = 0.3187 r_free = 0.3187 target = 0.055685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.044690 restraints weight = 24231.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.046690 restraints weight = 13722.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.048136 restraints weight = 9078.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.049085 restraints weight = 6588.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.049933 restraints weight = 5167.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.4752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4638  Z= 0.120
  Angle     :  0.567   7.649   6266  Z= 0.281
  Chirality :  0.042   0.174    682
  Planarity :  0.004   0.055    801
  Dihedral  :  4.858  29.199    636
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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:  0.09 (0.36), residues: 554
  helix:  1.03 (0.36), residues: 230
  sheet: -0.68 (0.65), residues: 64
  loop : -0.56 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 878 
 TYR   0.012   0.001   TYR A 889 
 PHE   0.009   0.001   PHE A 891 
 TRP   0.006   0.001   TRP A 861 
 HIS   0.002   0.001   HIS A 862 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4638)
  covalent geometry    : angle       0.56658 ( 6266)
  hydrogen bonds       : bond        0.03346 (  188)
  hydrogen bonds       : angle       5.22693 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  669 VAL cc_start: 0.9710 (t) cc_final: 0.9493 (t)
REVERT: A  672 LEU cc_start: 0.9716 (tp) cc_final: 0.9450 (pp)
REVERT: A  791 ASP cc_start: 0.8998 (t0) cc_final: 0.8598 (t70)
REVERT: A  837 PHE cc_start: 0.7784 (m-80) cc_final: 0.7352 (m-80)
REVERT: A  840 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8035 (mm-30)
REVERT: A  903 LYS cc_start: 0.9565 (tppp) cc_final: 0.9067 (tppt)
REVERT: A  912 GLN cc_start: 0.9597 (tm-30) cc_final: 0.9353 (mm-40)
REVERT: A  929 MET cc_start: 0.7732 (mtt) cc_final: 0.7137 (mmm)
REVERT: A  946 HIS cc_start: 0.9271 (m170) cc_final: 0.8962 (m90)
REVERT: A 1003 LEU cc_start: 0.9386 (mt) cc_final: 0.9115 (mt)
REVERT: B   56 PHE cc_start: 0.9528 (t80) cc_final: 0.8789 (t80)
REVERT: B   60 CYS cc_start: 0.9602 (m) cc_final: 0.9238 (m)
REVERT: B  169 LEU cc_start: 0.9497 (tp) cc_final: 0.9087 (pp)
REVERT: B  274 MET cc_start: 0.9355 (mmt) cc_final: 0.8839 (mmm)
REVERT: B  317 TYR cc_start: 0.9110 (m-10) cc_final: 0.7851 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0375
  time to fit residues: 3.2965
Evaluate side-chains
  42 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 45 optimal weight:    0.1980
   chunk 15 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 103 ASN ** 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 = 0.3202 r_free = 0.3202 target = 0.056233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.045287 restraints weight = 24109.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.047298 restraints weight = 13632.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.048806 restraints weight = 9048.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.049852 restraints weight = 6543.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.050700 restraints weight = 5082.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4638  Z= 0.112
  Angle     :  0.559   7.138   6266  Z= 0.277
  Chirality :  0.042   0.171    682
  Planarity :  0.004   0.056    801
  Dihedral  :  4.748  26.364    636
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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:  0.06 (0.35), residues: 554
  helix:  0.96 (0.35), residues: 230
  sheet: -0.61 (0.64), residues: 63
  loop : -0.55 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.016   0.002   TYR B  45 
 PHE   0.019   0.002   PHE A 897 
 TRP   0.006   0.001   TRP A 861 
 HIS   0.002   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4638)
  covalent geometry    : angle       0.55906 ( 6266)
  hydrogen bonds       : bond        0.03304 (  188)
  hydrogen bonds       : angle       5.21153 (  549)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  669 VAL cc_start: 0.9712 (t) cc_final: 0.9492 (t)
REVERT: A  672 LEU cc_start: 0.9715 (tp) cc_final: 0.9497 (pp)
REVERT: A  791 ASP cc_start: 0.8999 (t0) cc_final: 0.8746 (m-30)
REVERT: A  837 PHE cc_start: 0.7626 (m-80) cc_final: 0.7205 (m-80)
REVERT: A  840 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8003 (mm-30)
REVERT: A  903 LYS cc_start: 0.9567 (tppp) cc_final: 0.8999 (tppt)
REVERT: A  912 GLN cc_start: 0.9581 (tm-30) cc_final: 0.9346 (mm-40)
REVERT: A  929 MET cc_start: 0.7591 (mtt) cc_final: 0.6978 (mmm)
REVERT: A  946 HIS cc_start: 0.9263 (m170) cc_final: 0.8967 (m90)
REVERT: A 1003 LEU cc_start: 0.9387 (mt) cc_final: 0.9127 (mt)
REVERT: B   56 PHE cc_start: 0.9522 (t80) cc_final: 0.8771 (t80)
REVERT: B   60 CYS cc_start: 0.9588 (m) cc_final: 0.9213 (m)
REVERT: B  169 LEU cc_start: 0.9482 (tp) cc_final: 0.9068 (pp)
REVERT: B  274 MET cc_start: 0.9347 (mmt) cc_final: 0.8841 (mmm)
REVERT: B  275 MET cc_start: 0.9745 (ptm) cc_final: 0.9484 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0419
  time to fit residues: 3.6653
Evaluate side-chains
  43 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 272 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 = 0.3185 r_free = 0.3185 target = 0.055659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.044720 restraints weight = 24449.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.046736 restraints weight = 13796.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.048167 restraints weight = 9097.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.049295 restraints weight = 6609.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.050058 restraints weight = 5100.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4638  Z= 0.124
  Angle     :  0.575  11.201   6266  Z= 0.282
  Chirality :  0.042   0.169    682
  Planarity :  0.004   0.055    801
  Dihedral  :  4.724  25.741    636
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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:  0.03 (0.35), residues: 554
  helix:  0.93 (0.35), residues: 230
  sheet: -0.63 (0.64), residues: 63
  loop : -0.56 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 878 
 TYR   0.016   0.002   TYR B  45 
 PHE   0.019   0.002   PHE A 897 
 TRP   0.007   0.001   TRP A 861 
 HIS   0.002   0.001   HIS A 862 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4638)
  covalent geometry    : angle       0.57508 ( 6266)
  hydrogen bonds       : bond        0.03319 (  188)
  hydrogen bonds       : angle       5.24243 (  549)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 843.65 seconds
wall clock time: 15 minutes 17.77 seconds (917.77 seconds total)