Starting phenix.real_space_refine
on Tue Feb  3 16:15:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l05_62687/02_2026/9l05_62687.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l05_62687/02_2026/9l05_62687.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l05_62687/02_2026/9l05_62687.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l05_62687/02_2026/9l05_62687.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l05_62687/02_2026/9l05_62687.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l05_62687/02_2026/9l05_62687.cif"
  }
  resolution = 3.24
  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=   0.006
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      19      5.16       5
     C    2970      2.51       5
     N     780      2.21       5
     O     919      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 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: 4688
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "L"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1604
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 15, 'TRANS': 197}
    Chain: "H"
      Number of atoms: 1610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1610
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 13, 'TRANS': 198}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1474
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 12, 'TRANS': 171}
          Chain breaks: 1
  Time building chain proxies: 1.23, per 1000 atoms: 0.26
  Number of scatterers: 4688
  At special positions: 0
  Unit cell: (75.492, 116.5, 82.016, 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      19     16.00
     O     919      8.00
     N     780      7.00
     C    2970      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 155 " - pdb=" SG  CYS L 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 155 " - pdb=" SG  CYS H 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  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: 0.38
  Conformation dependent library (CDL) restraints added in 320.2 milliseconds
  

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1136

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 14 sheets defined
      8.5% alpha, 37.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'L' and resid 142 through 147
      removed outlier: 3.548A  pdb=" N   LEU L 146 " --> pdb=" O   SER L 142 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 202 through 209
    Processing helix  chain 'H' and resid 95 through 99
      removed outlier: 3.669A  pdb=" N   THR H  99 " --> pdb=" O   VAL H  96 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 201 through 205
      removed outlier: 3.629A  pdb=" N   LEU H 204 " --> pdb=" O   SER H 201 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY H 205 " --> pdb=" O   SER H 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 201 through 205'
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 4.090A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
      removed outlier: 3.815A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 406 through 410
    Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11
      removed outlier: 3.541A  pdb=" N   VAL L  11 " --> pdb=" O   GLN L 123 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   TRP L  41 " --> pdb=" O   VAL L  53 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 11
      removed outlier: 3.541A  pdb=" N   VAL L  11 " --> pdb=" O   GLN L 123 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL L 115 " --> pdb=" O   ASP L 108 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 24
    Processing sheet with id=AA4, first strand: chain 'L' and resid 135 through 139
      removed outlier: 3.534A  pdb=" N   PHE L 139 " --> pdb=" O   VAL L 154 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   VAL L 154 " --> pdb=" O   PHE L 139 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TYR L 193 " --> pdb=" O   ASP L 159 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 135 through 139
      removed outlier: 3.534A  pdb=" N   PHE L 139 " --> pdb=" O   VAL L 154 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   VAL L 154 " --> pdb=" O   PHE L 139 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TYR L 193 " --> pdb=" O   ASP L 159 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 175 through 176
      removed outlier: 4.138A  pdb=" N   TRP L 169 " --> pdb=" O   VAL L 176 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS L 170 " --> pdb=" O   SER L 213 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER L 213 " --> pdb=" O   LYS L 170 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL L 227 " --> pdb=" O   TYR L 212 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL L 223 " --> pdb=" O   VAL L 216 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER L 221 " --> pdb=" O   HIS L 218 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.588A  pdb=" N   GLN H   5 " --> pdb=" O   THR H  24 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 12 through 13
      removed outlier: 6.146A  pdb=" N   TRP H  39 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   TYR H  55 " --> pdb=" O   TRP H  39 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   TRP H  41 " --> pdb=" O   ILE H  53 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 12 through 13
      removed outlier: 3.901A  pdb=" N   HIS H 117 " --> pdb=" O   ARG H 106 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ASP H 108 " --> pdb=" O   PHE H 115 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   PHE H 115 " --> pdb=" O   ASP H 108 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 137 through 139
      removed outlier: 3.773A  pdb=" N   GLY H 154 " --> pdb=" O   LEU H 139 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ALA H 151 " --> pdb=" O   VAL H 199 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER H 195 " --> pdb=" O   CYS H 155 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 167 through 169
    Processing sheet with id=AB3, first strand: chain 'A' and resid 356 through 358
      removed outlier: 4.030A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   THR A 430 " --> pdb=" O   PHE A 515 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474

    163 hydrogen bonds defined for protein.
    390 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: 0.97

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1491
        1.34 -     1.46: 1174
        1.46 -     1.58: 2123
        1.58 -     1.69: 0
        1.69 -     1.81: 23
  Bond restraints: 4811
  Sorted by residual:
  bond pdb=" CA  VAL L 216 "
       pdb=" CB  VAL L 216 "
    ideal  model  delta    sigma   weight residual
    1.528  1.537 -0.009 1.34e-02 5.57e+03 4.48e-01
  bond pdb=" C   TYR L 161 "
       pdb=" N   PRO L 162 "
    ideal  model  delta    sigma   weight residual
    1.334  1.348 -0.015 2.34e-02 1.83e+03 3.88e-01
  bond pdb=" N   SER L 143 "
       pdb=" CA  SER L 143 "
    ideal  model  delta    sigma   weight residual
    1.457  1.464 -0.007 1.29e-02 6.01e+03 3.02e-01
  bond pdb=" CA  VAL L 216 "
       pdb=" C   VAL L 216 "
    ideal  model  delta    sigma   weight residual
    1.526  1.520  0.005 1.00e-02 1.00e+04 2.88e-01
  bond pdb=" CZ  ARG A 466 "
       pdb=" NH2 ARG A 466 "
    ideal  model  delta    sigma   weight residual
    1.330  1.323  0.007 1.30e-02 5.92e+03 2.65e-01
  ... (remaining 4806 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 6398
        1.25 -     2.51: 127
        2.51 -     3.76: 33
        3.76 -     5.02: 7
        5.02 -     6.27: 2
  Bond angle restraints: 6567
  Sorted by residual:
  angle pdb=" C   GLU L  56 "
        pdb=" N   ASN L  57 "
        pdb=" CA  ASN L  57 "
      ideal   model   delta    sigma   weight residual
     121.54  126.19   -4.65 1.91e+00 2.74e-01 5.92e+00
  angle pdb=" N   VAL L 216 "
        pdb=" CA  VAL L 216 "
        pdb=" C   VAL L 216 "
      ideal   model   delta    sigma   weight residual
     106.32  109.58   -3.26 1.61e+00 3.86e-01 4.10e+00
  angle pdb=" C   SER L 142 "
        pdb=" N   SER L 143 "
        pdb=" CA  SER L 143 "
      ideal   model   delta    sigma   weight residual
     121.54  125.36   -3.82 1.91e+00 2.74e-01 3.99e+00
  angle pdb=" N   PHE H 161 "
        pdb=" CA  PHE H 161 "
        pdb=" C   PHE H 161 "
      ideal   model   delta    sigma   weight residual
     109.81  114.13   -4.32 2.21e+00 2.05e-01 3.83e+00
  angle pdb=" O   ASP A 442 "
        pdb=" C   ASP A 442 "
        pdb=" N   SER A 443 "
      ideal   model   delta    sigma   weight residual
     122.19  124.50   -2.31 1.21e+00 6.83e-01 3.66e+00
  ... (remaining 6562 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.38: 2557
        9.38 -    18.76: 203
       18.76 -    28.14: 62
       28.14 -    37.52: 29
       37.52 -    46.90: 10
  Dihedral angle restraints: 2861
    sinusoidal: 1085
      harmonic: 1776
  Sorted by residual:
  dihedral pdb=" CA  VAL H 112 "
           pdb=" C   VAL H 112 "
           pdb=" N   SER H 113 "
           pdb=" CA  SER H 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.46  -16.54     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" N   THR L 183 "
           pdb=" CA  THR L 183 "
           pdb=" CB  THR L 183 "
           pdb=" OG1 THR L 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  104.34  -44.34     3      1.50e+01 4.44e-03 7.97e+00
  dihedral pdb=" N   LEU L 153 "
           pdb=" CA  LEU L 153 "
           pdb=" CB  LEU L 153 "
           pdb=" CG  LEU L 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.84  -44.16     3      1.50e+01 4.44e-03 7.94e+00
  ... (remaining 2858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 387
       0.025 -    0.049: 187
       0.049 -    0.074: 75
       0.074 -    0.098: 44
       0.098 -    0.123: 38
  Chirality restraints: 731
  Sorted by residual:
  chirality pdb=" CA  ILE L  91 "
            pdb=" N   ILE L  91 "
            pdb=" C   ILE L  91 "
            pdb=" CB  ILE L  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  chirality pdb=" CA  VAL L  11 "
            pdb=" N   VAL L  11 "
            pdb=" C   VAL L  11 "
            pdb=" CB  VAL L  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.69e-01
  chirality pdb=" CA  VAL A 511 "
            pdb=" N   VAL A 511 "
            pdb=" C   VAL A 511 "
            pdb=" CB  VAL A 511 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.56e-01
  ... (remaining 728 not shown)

  Planarity restraints: 845
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L 140 "   -0.025 5.00e-02 4.00e+02   3.83e-02 2.35e+00
        pdb=" N   PRO L 141 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO L 141 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO L 141 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 216 "   -0.019 5.00e-02 4.00e+02   2.79e-02 1.24e+00
        pdb=" N   PRO H 217 "    0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO H 217 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO H 217 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 199 "   -0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO H 200 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO H 200 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO H 200 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 842 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 603
        2.76 -     3.29: 4501
        3.29 -     3.83: 7638
        3.83 -     4.36: 9065
        4.36 -     4.90: 15991
  Nonbonded interactions: 37798
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OH  TYR L 107 "
            pdb=" O   SER H 113 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   ASP L  98 "
            pdb=" OH  TYR L 102 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASN L 114 "
            pdb=" OH  TYR H  55 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   SER L 142 "
            pdb=" N   GLU L 145 "
     model   vdw
     2.290 3.120
  ... (remaining 37793 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             31.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.640
  Find NCS groups from input model:        0.030
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6437
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   4818  Z= 0.096
  Angle     :  0.487   6.273   6581  Z= 0.257
  Chirality :  0.043   0.123    731
  Planarity :  0.004   0.038    845
  Dihedral  :  8.794  46.903   1704
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.70 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  :  4.91 %
    Favored  : 92.45 %
  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: -3.69 (0.28), residues: 597
  helix: -4.57 (0.30), residues: 26
  sheet: -1.97 (0.29), residues: 222
  loop : -2.67 (0.28), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.014   0.001   TYR H  55 
 PHE   0.008   0.001   PHE L 160 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.001   0.000   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 4811)
  covalent geometry    : angle       0.48755 ( 6567)
  SS BOND              : bond        0.00154 (    7)
  SS BOND              : angle       0.40823 (   14)
  hydrogen bonds       : bond        0.25268 (  145)
  hydrogen bonds       : angle      10.89823 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.178 
Fit side-chains
REVERT: H   86 GLN cc_start: 0.7770 (mt0) cc_final: 0.7217 (mt0)
REVERT: H  111 THR cc_start: 0.7715 (p) cc_final: 0.7504 (p)
REVERT: H  226 VAL cc_start: 0.7682 (t) cc_final: 0.7452 (m)
REVERT: A  421 TYR cc_start: 0.7815 (m-10) cc_final: 0.7510 (m-80)
REVERT: A  439 ASN cc_start: 0.7909 (t0) cc_final: 0.7559 (t0)
  outliers start: 14
  outliers final: 5
  residues processed: 126
  average time/residue: 0.0637
  time to fit residues: 10.6566
Evaluate side-chains
  101 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  104 CYS
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0870
   chunk 48 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0970
   chunk 2 optimal weight:    0.2980
   chunk 16 optimal weight:    0.0010
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    0.2980
   chunk 25 optimal weight:    0.1980
   chunk 58 optimal weight:    0.0170
   overall best weight:    0.0600

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

Flipped N/Q/H residues before XYZ refinement:
L 123 GLN
L 215 GLN
** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
H  48 GLN
H 120 GLN
A 422 ASN
A 487 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.163595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.148429 restraints weight = 7251.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 2.11
r_work: 0.3878 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3735 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6769
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4818  Z= 0.101
  Angle     :  0.561   5.640   6581  Z= 0.283
  Chirality :  0.046   0.173    731
  Planarity :  0.004   0.030    845
  Dihedral  :  5.046  46.133    666
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 11.51 %
    Favored  : 85.66 %
  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: -2.58 (0.31), residues: 597
  helix: -3.93 (0.54), residues: 20
  sheet: -1.36 (0.32), residues: 227
  loop : -1.84 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  75 
 TYR   0.013   0.001   TYR H  66 
 PHE   0.012   0.001   PHE H  87 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.001   0.000   HIS L 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 4811)
  covalent geometry    : angle       0.56101 ( 6567)
  SS BOND              : bond        0.00219 (    7)
  SS BOND              : angle       0.42864 (   14)
  hydrogen bonds       : bond        0.03550 (  145)
  hydrogen bonds       : angle       7.40761 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.169 
Fit side-chains
REVERT: L   17 MET cc_start: 0.7805 (mmm) cc_final: 0.7554 (mmm)
REVERT: H   46 PRO cc_start: 0.8407 (Cg_endo) cc_final: 0.8188 (Cg_exo)
REVERT: H   87 PHE cc_start: 0.8009 (p90) cc_final: 0.7688 (p90)
REVERT: H  226 VAL cc_start: 0.7674 (t) cc_final: 0.7325 (m)
REVERT: A  421 TYR cc_start: 0.7844 (m-10) cc_final: 0.7479 (m-80)
REVERT: A  439 ASN cc_start: 0.8031 (t0) cc_final: 0.7815 (t0)
  outliers start: 15
  outliers final: 12
  residues processed: 105
  average time/residue: 0.0685
  time to fit residues: 9.4092
Evaluate side-chains
  96 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  104 CYS
Chi-restraints excluded: chain L residue  113 SER
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  186 SER
Chi-restraints excluded: chain L residue  213 SER
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  122 ILE
Chi-restraints excluded: chain H residue  180 THR
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0980
   chunk 57 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0000
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0870
   chunk 55 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.2762

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

Flipped N/Q/H residues before XYZ refinement:
** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 179 HIS
A 360 ASN
A 505 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.158697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.143709 restraints weight = 7198.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 2.08
r_work: 0.3819 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3675 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   4818  Z= 0.212
  Angle     :  0.652   9.820   6581  Z= 0.331
  Chirality :  0.049   0.191    731
  Planarity :  0.005   0.034    845
  Dihedral  :  5.987  59.500    666
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 11.70 %
    Favored  : 82.64 %
  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: -2.41 (0.32), residues: 597
  helix: -3.63 (0.62), residues: 20
  sheet: -1.22 (0.33), residues: 222
  loop : -1.75 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 454 
 TYR   0.023   0.002   TYR H  55 
 PHE   0.017   0.002   PHE L 139 
 TRP   0.020   0.002   TRP A 436 
 HIS   0.003   0.001   HIS L 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 4811)
  covalent geometry    : angle       0.65168 ( 6567)
  SS BOND              : bond        0.00385 (    7)
  SS BOND              : angle       0.73700 (   14)
  hydrogen bonds       : bond        0.03597 (  145)
  hydrogen bonds       : angle       7.02166 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 MET cc_start: 0.7801 (mmm) cc_final: 0.7554 (mmm)
REVERT: H   87 PHE cc_start: 0.8099 (p90) cc_final: 0.7637 (p90)
REVERT: H  226 VAL cc_start: 0.7829 (t) cc_final: 0.7546 (m)
REVERT: A  439 ASN cc_start: 0.8159 (t0) cc_final: 0.7930 (t0)
  outliers start: 30
  outliers final: 19
  residues processed: 106
  average time/residue: 0.0629
  time to fit residues: 8.9191
Evaluate side-chains
  106 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  104 CYS
Chi-restraints excluded: chain L residue  135 SER
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  197 SER
Chi-restraints excluded: chain L residue  213 SER
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  122 ILE
Chi-restraints excluded: chain H residue  180 THR
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:    0.0670
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 53 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 29 optimal weight:    0.0980
   chunk 59 optimal weight:    0.0370
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0570
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.1314

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

Flipped N/Q/H residues before XYZ refinement:
** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.160875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.145799 restraints weight = 7269.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 2.13
r_work: 0.3841 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3696 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4818  Z= 0.125
  Angle     :  0.582   9.520   6581  Z= 0.295
  Chirality :  0.047   0.159    731
  Planarity :  0.004   0.032    845
  Dihedral  :  5.662  59.942    666
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 12.83 %
    Favored  : 82.64 %
  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: -2.06 (0.33), residues: 597
  helix: -3.37 (0.69), residues: 20
  sheet: -0.99 (0.32), residues: 236
  loop : -1.50 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  75 
 TYR   0.016   0.001   TYR H  38 
 PHE   0.012   0.001   PHE L 139 
 TRP   0.013   0.002   TRP A 353 
 HIS   0.003   0.001   HIS H 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4811)
  covalent geometry    : angle       0.58256 ( 6567)
  SS BOND              : bond        0.00209 (    7)
  SS BOND              : angle       0.51443 (   14)
  hydrogen bonds       : bond        0.02774 (  145)
  hydrogen bonds       : angle       6.63349 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 MET cc_start: 0.7738 (mmm) cc_final: 0.7493 (mmm)
REVERT: H    5 GLN cc_start: 0.7996 (tp40) cc_final: 0.7669 (tp40)
REVERT: H   87 PHE cc_start: 0.8058 (p90) cc_final: 0.7760 (p90)
REVERT: H  179 HIS cc_start: 0.6421 (t-90) cc_final: 0.5859 (t70)
REVERT: H  226 VAL cc_start: 0.7697 (t) cc_final: 0.7384 (m)
  outliers start: 24
  outliers final: 19
  residues processed: 103
  average time/residue: 0.0571
  time to fit residues: 7.9566
Evaluate side-chains
  107 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  104 CYS
Chi-restraints excluded: chain L residue  135 SER
Chi-restraints excluded: chain L residue  157 ILE
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  213 SER
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  122 ILE
Chi-restraints excluded: chain H residue  180 THR
Chi-restraints excluded: chain H residue  185 LEU
Chi-restraints excluded: chain H residue  187 SER
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0000
   chunk 0 optimal weight:    0.0670
   chunk 47 optimal weight:    0.0870
   chunk 32 optimal weight:    0.0570
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.1218

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

Flipped N/Q/H residues before XYZ refinement:
L 209 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.160929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.146029 restraints weight = 7179.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.11
r_work: 0.3850 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3710 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4818  Z= 0.121
  Angle     :  0.580   9.251   6581  Z= 0.295
  Chirality :  0.047   0.179    731
  Planarity :  0.004   0.032    845
  Dihedral  :  5.450  51.378    666
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.87 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.28 %
    Favored  : 80.38 %
  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: -1.80 (0.33), residues: 597
  helix: -3.15 (0.74), residues: 20
  sheet: -0.77 (0.33), residues: 236
  loop : -1.36 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  75 
 TYR   0.018   0.002   TYR H  38 
 PHE   0.010   0.001   PHE H  87 
 TRP   0.013   0.002   TRP A 353 
 HIS   0.002   0.000   HIS H 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4811)
  covalent geometry    : angle       0.57961 ( 6567)
  SS BOND              : bond        0.00215 (    7)
  SS BOND              : angle       0.56371 (   14)
  hydrogen bonds       : bond        0.02678 (  145)
  hydrogen bonds       : angle       6.22703 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 MET cc_start: 0.7743 (mmm) cc_final: 0.7496 (mmm)
REVERT: H    5 GLN cc_start: 0.8031 (tp40) cc_final: 0.7761 (tp40)
REVERT: H  158 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7847 (ttpp)
REVERT: H  179 HIS cc_start: 0.6383 (t-90) cc_final: 0.5830 (t70)
REVERT: H  226 VAL cc_start: 0.7719 (t) cc_final: 0.7412 (m)
REVERT: A  444 LYS cc_start: 0.7204 (ptpp) cc_final: 0.6796 (ptpp)
  outliers start: 23
  outliers final: 18
  residues processed: 104
  average time/residue: 0.0636
  time to fit residues: 8.7871
Evaluate side-chains
  103 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  104 CYS
Chi-restraints excluded: chain L residue  135 SER
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  197 SER
Chi-restraints excluded: chain L residue  213 SER
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  122 ILE
Chi-restraints excluded: chain H residue  180 THR
Chi-restraints excluded: chain H residue  212 ASN
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 53 optimal weight:    0.4980
   chunk 12 optimal weight:    0.5980
   chunk 1 optimal weight:    0.2980
   chunk 52 optimal weight:    0.0970
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** L 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 209 HIS
** A 439 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 = 0.4060 r_free = 0.4060 target = 0.156612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.141935 restraints weight = 7347.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 2.12
r_work: 0.3758 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3607 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067   4818  Z= 0.310
  Angle     :  0.755  10.946   6581  Z= 0.387
  Chirality :  0.052   0.201    731
  Planarity :  0.005   0.037    845
  Dihedral  :  6.383  53.568    666
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  9.05 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 14.15 %
    Favored  : 80.00 %
  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: -2.09 (0.32), residues: 597
  helix: -3.16 (0.78), residues: 20
  sheet: -0.94 (0.32), residues: 236
  loop : -1.61 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 454 
 TYR   0.031   0.003   TYR H  38 
 PHE   0.018   0.003   PHE L 160 
 TRP   0.024   0.003   TRP A 436 
 HIS   0.004   0.001   HIS L 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 ( 4811)
  covalent geometry    : angle       0.75394 ( 6567)
  SS BOND              : bond        0.00553 (    7)
  SS BOND              : angle       0.99943 (   14)
  hydrogen bonds       : bond        0.03581 (  145)
  hydrogen bonds       : angle       6.59336 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 MET cc_start: 0.7806 (mmm) cc_final: 0.7561 (mmm)
REVERT: H    5 GLN cc_start: 0.8027 (tp40) cc_final: 0.7745 (tp40)
REVERT: H   86 GLN cc_start: 0.8224 (mt0) cc_final: 0.7941 (mt0)
REVERT: H  226 VAL cc_start: 0.7914 (t) cc_final: 0.7665 (m)
  outliers start: 31
  outliers final: 23
  residues processed: 116
  average time/residue: 0.0650
  time to fit residues: 10.1055
Evaluate side-chains
  116 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  104 CYS
Chi-restraints excluded: chain L residue  138 LEU
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  213 SER
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   36 TYR
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  122 ILE
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  180 THR
Chi-restraints excluded: chain H residue  187 SER
Chi-restraints excluded: chain H residue  212 ASN
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 4 optimal weight:    0.2980
   chunk 14 optimal weight:    0.0970
   chunk 45 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0980
   chunk 50 optimal weight:    0.3980
   chunk 7 optimal weight:    0.5980
   chunk 53 optimal weight:    0.2980
   chunk 28 optimal weight:    0.0670
   chunk 46 optimal weight:    0.0870
   overall best weight:    0.1294

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

Flipped N/Q/H residues before XYZ refinement:
** L 188 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 = 0.4110 r_free = 0.4110 target = 0.160323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.145664 restraints weight = 7156.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.11
r_work: 0.3833 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3687 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4818  Z= 0.134
  Angle     :  0.624   9.083   6581  Z= 0.318
  Chirality :  0.049   0.186    731
  Planarity :  0.005   0.036    845
  Dihedral  :  5.869  47.417    666
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.36 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 15.47 %
    Favored  : 79.81 %
  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: -1.85 (0.33), residues: 597
  helix: -2.78 (0.91), residues: 20
  sheet: -0.82 (0.33), residues: 235
  loop : -1.41 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 466 
 TYR   0.019   0.002   TYR H  38 
 PHE   0.012   0.001   PHE L 160 
 TRP   0.015   0.002   TRP H  52 
 HIS   0.002   0.001   HIS H 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4811)
  covalent geometry    : angle       0.62438 ( 6567)
  SS BOND              : bond        0.00226 (    7)
  SS BOND              : angle       0.55171 (   14)
  hydrogen bonds       : bond        0.02760 (  145)
  hydrogen bonds       : angle       6.33546 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 MET cc_start: 0.7848 (mmm) cc_final: 0.7595 (mmm)
REVERT: H    5 GLN cc_start: 0.7979 (tp40) cc_final: 0.7746 (tp40)
REVERT: H  179 HIS cc_start: 0.6361 (t-90) cc_final: 0.5804 (t70)
REVERT: H  226 VAL cc_start: 0.7729 (t) cc_final: 0.7452 (m)
  outliers start: 25
  outliers final: 19
  residues processed: 108
  average time/residue: 0.0709
  time to fit residues: 9.8848
Evaluate side-chains
  104 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  104 CYS
Chi-restraints excluded: chain L residue  135 SER
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  199 LEU
Chi-restraints excluded: chain L residue  213 SER
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  122 ILE
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  185 LEU
Chi-restraints excluded: chain H residue  212 ASN
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    0.0010
   chunk 8 optimal weight:    0.0020
   chunk 31 optimal weight:    0.1980
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0170
   chunk 32 optimal weight:    0.0980
   chunk 50 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.0632

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

Flipped N/Q/H residues before XYZ refinement:
** L 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 218 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 = 0.4140 r_free = 0.4140 target = 0.162686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.147883 restraints weight = 7314.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 2.15
r_work: 0.3867 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3720 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4818  Z= 0.103
  Angle     :  0.592   7.912   6581  Z= 0.300
  Chirality :  0.048   0.192    731
  Planarity :  0.005   0.036    845
  Dihedral  :  5.550  46.408    666
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.19 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.04 %
    Favored  : 80.75 %
  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: -1.58 (0.33), residues: 597
  helix: -2.83 (0.90), residues: 20
  sheet: -0.51 (0.34), residues: 232
  loop : -1.32 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 355 
 TYR   0.015   0.001   TYR H  38 
 PHE   0.011   0.001   PHE H  87 
 TRP   0.013   0.001   TRP H  52 
 HIS   0.001   0.000   HIS H 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 4811)
  covalent geometry    : angle       0.59203 ( 6567)
  SS BOND              : bond        0.00134 (    7)
  SS BOND              : angle       0.51695 (   14)
  hydrogen bonds       : bond        0.02474 (  145)
  hydrogen bonds       : angle       6.11357 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 MET cc_start: 0.7812 (mmm) cc_final: 0.7557 (mmm)
REVERT: L  213 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7686 (m)
REVERT: H   66 TYR cc_start: 0.6720 (m-80) cc_final: 0.6485 (m-80)
REVERT: H  179 HIS cc_start: 0.6026 (t-90) cc_final: 0.5457 (t70)
REVERT: H  226 VAL cc_start: 0.7661 (t) cc_final: 0.7354 (m)
  outliers start: 17
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0725
  time to fit residues: 9.0006
Evaluate side-chains
  93 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  199 LEU
Chi-restraints excluded: chain L residue  213 SER
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   55 TYR
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  122 ILE
Chi-restraints excluded: chain H residue  185 LEU
Chi-restraints excluded: chain H residue  212 ASN
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0000
   chunk 7 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0980
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 30 optimal weight:    0.4980
   chunk 15 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0970
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.2582

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

Flipped N/Q/H residues before XYZ refinement:
** L 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 HIS
** A 439 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 = 0.4085 r_free = 0.4085 target = 0.158599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.144030 restraints weight = 7146.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.09
r_work: 0.3792 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   4818  Z= 0.207
  Angle     :  0.678   9.524   6581  Z= 0.344
  Chirality :  0.050   0.240    731
  Planarity :  0.005   0.044    845
  Dihedral  :  5.752  40.181    665
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.37 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.42 %
    Favored  : 80.00 %
  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: -1.65 (0.34), residues: 597
  helix: -2.82 (0.93), residues: 20
  sheet: -0.62 (0.34), residues: 235
  loop : -1.31 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 355 
 TYR   0.027   0.002   TYR H  38 
 PHE   0.016   0.002   PHE L 160 
 TRP   0.021   0.002   TRP A 353 
 HIS   0.002   0.001   HIS H 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 4811)
  covalent geometry    : angle       0.67784 ( 6567)
  SS BOND              : bond        0.00373 (    7)
  SS BOND              : angle       0.84382 (   14)
  hydrogen bonds       : bond        0.02985 (  145)
  hydrogen bonds       : angle       6.25832 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 MET cc_start: 0.7804 (mmm) cc_final: 0.7567 (mmm)
REVERT: H  226 VAL cc_start: 0.7782 (t) cc_final: 0.7516 (m)
  outliers start: 19
  outliers final: 16
  residues processed: 101
  average time/residue: 0.0621
  time to fit residues: 8.5189
Evaluate side-chains
  102 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  199 LEU
Chi-restraints excluded: chain L residue  213 SER
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   55 TYR
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  122 ILE
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  187 SER
Chi-restraints excluded: chain H residue  212 ASN
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0670
   chunk 55 optimal weight:    0.0000
   chunk 40 optimal weight:    0.0770
   chunk 12 optimal weight:    0.0980
   chunk 36 optimal weight:    0.2980
   chunk 34 optimal weight:    0.5980
   chunk 26 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.1080

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

Flipped N/Q/H residues before XYZ refinement:
** L 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 218 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 = 0.4128 r_free = 0.4128 target = 0.161537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.146818 restraints weight = 7234.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 2.10
r_work: 0.3856 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3712 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4818  Z= 0.122
  Angle     :  0.622   8.420   6581  Z= 0.313
  Chirality :  0.049   0.225    731
  Planarity :  0.005   0.037    845
  Dihedral  :  5.225  36.266    664
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.36 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.36 %
    Favored  : 79.81 %
  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: -1.52 (0.34), residues: 597
  helix: -2.69 (0.97), residues: 20
  sheet: -0.45 (0.34), residues: 230
  loop : -1.29 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 355 
 TYR   0.030   0.002   TYR H  38 
 PHE   0.011   0.001   PHE L 160 
 TRP   0.012   0.002   TRP H  52 
 HIS   0.002   0.001   HIS H 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4811)
  covalent geometry    : angle       0.62166 ( 6567)
  SS BOND              : bond        0.00187 (    7)
  SS BOND              : angle       0.66206 (   14)
  hydrogen bonds       : bond        0.02557 (  145)
  hydrogen bonds       : angle       6.02838 (  390)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 MET cc_start: 0.7859 (mmm) cc_final: 0.7597 (mmm)
REVERT: L  105 GLN cc_start: 0.7366 (tm-30) cc_final: 0.7089 (tm-30)
REVERT: L  213 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.7693 (m)
REVERT: H  226 VAL cc_start: 0.7679 (t) cc_final: 0.7390 (m)
  outliers start: 15
  outliers final: 13
  residues processed: 97
  average time/residue: 0.0452
  time to fit residues: 5.8722
Evaluate side-chains
  98 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  135 SER
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  199 LEU
Chi-restraints excluded: chain L residue  213 SER
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  122 ILE
Chi-restraints excluded: chain H residue  212 ASN
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    0.0870
   chunk 56 optimal weight:    0.0970
   chunk 35 optimal weight:    0.4980
   chunk 44 optimal weight:    0.0970
   chunk 26 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0970
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.3980
   chunk 33 optimal weight:    0.1980
   chunk 36 optimal weight:    0.0570
   overall best weight:    0.0870

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

Flipped N/Q/H residues before XYZ refinement:
** L 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 218 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 = 0.4139 r_free = 0.4139 target = 0.162636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.147826 restraints weight = 7256.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 2.12
r_work: 0.3863 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4818  Z= 0.112
  Angle     :  0.601   7.876   6581  Z= 0.305
  Chirality :  0.048   0.199    731
  Planarity :  0.004   0.037    845
  Dihedral  :  5.084  36.330    664
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.86 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.98 %
    Favored  : 79.62 %
  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: -1.31 (0.34), residues: 597
  helix: -2.45 (1.00), residues: 20
  sheet: -0.33 (0.34), residues: 235
  loop : -1.15 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 454 
 TYR   0.025   0.001   TYR H  38 
 PHE   0.011   0.001   PHE L 160 
 TRP   0.012   0.002   TRP H  52 
 HIS   0.001   0.000   HIS H 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4811)
  covalent geometry    : angle       0.60112 ( 6567)
  SS BOND              : bond        0.00185 (    7)
  SS BOND              : angle       0.58551 (   14)
  hydrogen bonds       : bond        0.02618 (  145)
  hydrogen bonds       : angle       5.85982 (  390)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2041.29 seconds
wall clock time: 35 minutes 53.72 seconds (2153.72 seconds total)