Starting phenix.real_space_refine
on Mon May 12 13:46:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9juk_61828/05_2025/9juk_61828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9juk_61828/05_2025/9juk_61828.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9juk_61828/05_2025/9juk_61828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9juk_61828/05_2025/9juk_61828.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9juk_61828/05_2025/9juk_61828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9juk_61828/05_2025/9juk_61828.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.005
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      41      5.16       5
     C    5756      2.51       5
     N    1555      2.21       5
     O    1675      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9035
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1165, 8971
          Classifications: {'peptide': 1165}
          Link IDs: {'PTRANS': 30, 'TRANS': 1134}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 64
          Unusual residues: {' MG': 2, 'ANP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 5.33, per 1000 atoms: 0.59
  Number of scatterers: 9035
  At special positions: 0
  Unit cell: (102.3, 101.37, 125.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      41     16.00
     P       6     15.00
     Mg      2     11.99
     O    1675      8.00
     N    1555      7.00
     C    5756      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: 2.65
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 5 sheets defined
      67.4% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 34
    Processing helix  chain 'A' and resid 37 through 75
      removed outlier: 4.120A  pdb=" N   LEU A  58 " --> pdb=" O   HIS A  54 " (cutoff:3.500A)
      Proline residue:  A  59  - end of helix
      removed outlier: 3.780A  pdb=" N   ASN A  75 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 133
    Processing helix  chain 'A' and resid 134 through 140
      removed outlier: 3.774A  pdb=" N   PHE A 138 " --> pdb=" O   ASP A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 4.671A  pdb=" N   ALA A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   VAL A 156 " --> pdb=" O   ASN A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 187
    Processing helix  chain 'A' and resid 187 through 236
      Proline residue:  A 199  - end of helix
    Processing helix  chain 'A' and resid 236 through 243
      removed outlier: 3.514A  pdb=" N   ALA A 242 " --> pdb=" O   ARG A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 299
    Processing helix  chain 'A' and resid 303 through 323
    Processing helix  chain 'A' and resid 324 through 347
      removed outlier: 3.747A  pdb=" N   HIS A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 3.956A  pdb=" N   ASN A 354 " --> pdb=" O   ILE A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 417
    Processing helix  chain 'A' and resid 440 through 446
      removed outlier: 3.931A  pdb=" N   GLN A 444 " --> pdb=" O   ARG A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 466
    Processing helix  chain 'A' and resid 472 through 483
      removed outlier: 3.757A  pdb=" N   ALA A 483 " --> pdb=" O   ALA A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 491
    Processing helix  chain 'A' and resid 509 through 523
      removed outlier: 3.505A  pdb=" N   LYS A 523 " --> pdb=" O   ARG A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 547
      removed outlier: 3.874A  pdb=" N   LYS A 543 " --> pdb=" O   SER A 539 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLU A 547 " --> pdb=" O   LYS A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 693
      removed outlier: 4.225A  pdb=" N   GLN A 682 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 729
      removed outlier: 3.507A  pdb=" N   TYR A 729 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 786
    Processing helix  chain 'A' and resid 788 through 794
      removed outlier: 3.508A  pdb=" N   PHE A 792 " --> pdb=" O   GLU A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 797
      No H-bonds generated for 'chain 'A' and resid 795 through 797'
    Processing helix  chain 'A' and resid 798 through 818
    Processing helix  chain 'A' and resid 818 through 842
    Processing helix  chain 'A' and resid 845 through 852
    Processing helix  chain 'A' and resid 852 through 869
    Processing helix  chain 'A' and resid 873 through 878
    Processing helix  chain 'A' and resid 878 through 891
    Processing helix  chain 'A' and resid 891 through 899
    Processing helix  chain 'A' and resid 900 through 954
      Proline residue:  A 914  - end of helix
    Processing helix  chain 'A' and resid 958 through 1001
      Proline residue:  A 984  - end of helix
    Processing helix  chain 'A' and resid 1064 through 1066
      No H-bonds generated for 'chain 'A' and resid 1064 through 1066'
    Processing helix  chain 'A' and resid 1067 through 1073
    Processing helix  chain 'A' and resid 1094 through 1100
    Processing helix  chain 'A' and resid 1115 through 1122
    Processing helix  chain 'A' and resid 1129 through 1139
    Processing helix  chain 'A' and resid 1142 through 1148
      removed outlier: 3.992A  pdb=" N   LEU A1148 " --> pdb=" O   PHE A1144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1180
      removed outlier: 3.537A  pdb=" N   LYS A1180 " --> pdb=" O   ALA A1176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1212
      removed outlier: 3.954A  pdb=" N   ARG A1212 " --> pdb=" O   ALA A1208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1255
      removed outlier: 4.297A  pdb=" N   GLY A1254 " --> pdb=" O   ASN A1250 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE A1255 " --> pdb=" O   HIS A1251 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1250 through 1255'
    Processing helix  chain 'A' and resid 1255 through 1264
      removed outlier: 4.102A  pdb=" N   MET A1259 " --> pdb=" O   ILE A1255 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE A1260 " --> pdb=" O   TYR A1256 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 370
    Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 400
      removed outlier: 6.213A  pdb=" N   ILE A 399 " --> pdb=" O   THR A 558 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 578
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1045 through 1049
      removed outlier: 3.530A  pdb=" N   LEU A1045 " --> pdb=" O   ILE A1029 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   LEU A1047 " --> pdb=" O   LYS A1027 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   LYS A1027 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   ALA A1049 " --> pdb=" O   GLU A1025 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   GLU A1025 " --> pdb=" O   ALA A1049 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1054 through 1055
      removed outlier: 6.354A  pdb=" N   MET A1184 " --> pdb=" O   ILE A1215 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ALA A1103 " --> pdb=" O   LEU A1185 " (cutoff:3.500A)

    596 hydrogen bonds defined for protein.
    1764 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: 3.06

  Time building geometry restraints manager: 2.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2952
        1.34 -     1.46: 1974
        1.46 -     1.58: 4199
        1.58 -     1.70: 10
        1.70 -     1.82: 68
  Bond restraints: 9203
  Sorted by residual:
  bond pdb=" N3B ANP A1304 "
       pdb=" PG  ANP A1304 "
    ideal  model  delta    sigma   weight residual
    1.795  1.631  0.164 2.00e-02 2.50e+03 6.70e+01
  bond pdb=" N3B ANP A1303 "
       pdb=" PG  ANP A1303 "
    ideal  model  delta    sigma   weight residual
    1.795  1.634  0.161 2.00e-02 2.50e+03 6.51e+01
  bond pdb=" O3A ANP A1304 "
       pdb=" PB  ANP A1304 "
    ideal  model  delta    sigma   weight residual
    1.700  1.601  0.099 2.00e-02 2.50e+03 2.44e+01
  bond pdb=" O3A ANP A1303 "
       pdb=" PB  ANP A1303 "
    ideal  model  delta    sigma   weight residual
    1.700  1.602  0.098 2.00e-02 2.50e+03 2.38e+01
  bond pdb=" N   VAL A 813 "
       pdb=" CA  VAL A 813 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.26e-02 6.30e+03 7.23e+00
  ... (remaining 9198 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 12216
        1.90 -     3.80: 196
        3.80 -     5.71: 42
        5.71 -     7.61: 13
        7.61 -     9.51: 3
  Bond angle restraints: 12470
  Sorted by residual:
  angle pdb=" CA  PRO A1034 "
        pdb=" N   PRO A1034 "
        pdb=" CD  PRO A1034 "
      ideal   model   delta    sigma   weight residual
     112.00  106.64    5.36 1.40e+00 5.10e-01 1.46e+01
  angle pdb=" N   GLU A 478 "
        pdb=" CA  GLU A 478 "
        pdb=" CB  GLU A 478 "
      ideal   model   delta    sigma   weight residual
     110.40  115.98   -5.58 1.63e+00 3.76e-01 1.17e+01
  angle pdb=" C   GLU A 477 "
        pdb=" N   GLU A 478 "
        pdb=" CA  GLU A 478 "
      ideal   model   delta    sigma   weight residual
     121.14  115.22    5.92 1.75e+00 3.27e-01 1.15e+01
  angle pdb=" N3B ANP A1304 "
        pdb=" PG  ANP A1304 "
        pdb=" O2G ANP A1304 "
      ideal   model   delta    sigma   weight residual
     101.05  110.56   -9.51 3.00e+00 1.11e-01 1.01e+01
  angle pdb=" N3B ANP A1303 "
        pdb=" PG  ANP A1303 "
        pdb=" O2G ANP A1303 "
      ideal   model   delta    sigma   weight residual
     101.05  110.25   -9.20 3.00e+00 1.11e-01 9.41e+00
  ... (remaining 12465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.16: 5219
       27.16 -    54.33: 237
       54.33 -    81.49: 59
       81.49 -   108.65: 10
      108.65 -   135.81: 2
  Dihedral angle restraints: 5527
    sinusoidal: 2173
      harmonic: 3354
  Sorted by residual:
  dihedral pdb=" O1A ANP A1303 "
           pdb=" O3A ANP A1303 "
           pdb=" PA  ANP A1303 "
           pdb=" PB  ANP A1303 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -52.70  135.81     1      3.00e+01 1.11e-03 1.83e+01
  dihedral pdb=" O1A ANP A1304 "
           pdb=" O3A ANP A1304 "
           pdb=" PA  ANP A1304 "
           pdb=" PB  ANP A1304 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -28.61  111.72     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" O1B ANP A1304 "
           pdb=" N3B ANP A1304 "
           pdb=" PB  ANP A1304 "
           pdb=" PG  ANP A1304 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15  -64.66   99.81     1      3.00e+01 1.11e-03 1.25e+01
  ... (remaining 5524 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1319
       0.070 -    0.139: 108
       0.139 -    0.208: 7
       0.208 -    0.278: 0
       0.278 -    0.347: 2
  Chirality restraints: 1436
  Sorted by residual:
  chirality pdb=" C3' ANP A1304 "
            pdb=" C2' ANP A1304 "
            pdb=" C4' ANP A1304 "
            pdb=" O3' ANP A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.70    0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" C3' ANP A1303 "
            pdb=" C2' ANP A1303 "
            pdb=" C4' ANP A1303 "
            pdb=" O3' ANP A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.65    0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CB  VAL A 500 "
            pdb=" CA  VAL A 500 "
            pdb=" CG1 VAL A 500 "
            pdb=" CG2 VAL A 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.92e-01
  ... (remaining 1433 not shown)

  Planarity restraints: 1574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A1033 "    0.083 5.00e-02 4.00e+02   1.23e-01 2.41e+01
        pdb=" N   PRO A1034 "   -0.212 5.00e-02 4.00e+02
        pdb=" CA  PRO A1034 "    0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO A1034 "    0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 393 "   -0.036 5.00e-02 4.00e+02   5.44e-02 4.74e+00
        pdb=" N   PRO A 394 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 394 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 394 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 721 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   LEU A 721 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   LEU A 721 "    0.011 2.00e-02 2.50e+03
        pdb=" N   SER A 722 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1571 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 88
        2.61 -     3.18: 8501
        3.18 -     3.75: 15156
        3.75 -     4.33: 19888
        4.33 -     4.90: 32706
  Nonbonded interactions: 76339
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 410 "
            pdb="MG    MG A1301 "
     model   vdw
     2.036 2.170
  nonbonded pdb=" OD2 ASP A 531 "
            pdb="MG    MG A1301 "
     model   vdw
     2.124 2.170
  nonbonded pdb=" OE1 GLN A1107 "
            pdb="MG    MG A1302 "
     model   vdw
     2.206 2.170
  nonbonded pdb=" OG1 THR A1013 "
            pdb=" OD1 ASN A1094 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OD1 ASN A 758 "
            pdb=" NE2 GLN A 761 "
     model   vdw
     2.240 3.120
  ... (remaining 76334 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.510
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6729
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.164   9203  Z= 0.226
  Angle     :  0.642   9.511  12470  Z= 0.336
  Chirality :  0.042   0.347   1436
  Planarity :  0.005   0.123   1574
  Dihedral  : 16.731 135.814   3369
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.42 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.25), residues: 1161
  helix:  1.80 (0.19), residues: 747
  sheet: -1.60 (1.19), residues: 27
  loop : -1.89 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 791 
 HIS   0.004   0.001   HIS A 762 
 PHE   0.024   0.001   PHE A 552 
 TYR   0.025   0.002   TYR A 908 
 ARG   0.003   0.000   ARG A 481 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10898 (  596)
  hydrogen bonds       : angle       4.83914 ( 1764)
  covalent geometry    : bond        0.00441 ( 9203)
  covalent geometry    : angle       0.64233 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.7705 (tp30) cc_final: 0.7265 (tp30)
REVERT: A  286 TYR cc_start: 0.6787 (m-10) cc_final: 0.6295 (m-80)
REVERT: A  315 MET cc_start: 0.7800 (mmt) cc_final: 0.7456 (mmm)
REVERT: A  344 ILE cc_start: 0.7541 (mp) cc_final: 0.7261 (mp)
REVERT: A  440 ARG cc_start: 0.7568 (ttp80) cc_final: 0.7260 (tpt170)
REVERT: A  686 PHE cc_start: 0.6437 (t80) cc_final: 0.6236 (t80)
REVERT: A  729 TYR cc_start: 0.6707 (m-80) cc_final: 0.6002 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2225
  time to fit residues: 39.3002
Evaluate side-chains
  109 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0040
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 90 optimal weight:    0.0060
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 105 optimal weight:   10.0000
   overall best weight:    0.7810

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
A 761 GLN
** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1094 ASN
** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.220936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.162219 restraints weight = 9305.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 1.80
r_work: 0.3842 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3720 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.0998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9203  Z= 0.122
  Angle     :  0.526   8.808  12470  Z= 0.276
  Chirality :  0.039   0.158   1436
  Planarity :  0.004   0.076   1574
  Dihedral  :  9.151 126.840   1318
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  7.17 %
    Favored  : 91.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.25), residues: 1161
  helix:  2.13 (0.19), residues: 754
  sheet: -1.02 (1.49), residues: 17
  loop : -1.90 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 188 
 HIS   0.003   0.001   HIS A 171 
 PHE   0.019   0.001   PHE A 552 
 TYR   0.017   0.001   TYR A 908 
 ARG   0.005   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04365 (  596)
  hydrogen bonds       : angle       3.96185 ( 1764)
  covalent geometry    : bond        0.00246 ( 9203)
  covalent geometry    : angle       0.52551 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.7363 (mmm) cc_final: 0.7115 (tpt)
REVERT: A  116 GLU cc_start: 0.8309 (tp30) cc_final: 0.7885 (tp30)
REVERT: A  141 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5290 (mp0)
REVERT: A  286 TYR cc_start: 0.7315 (m-10) cc_final: 0.6927 (m-80)
REVERT: A  440 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7246 (tpt170)
REVERT: A  478 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7341 (pm20)
REVERT: A  532 GLU cc_start: 0.6358 (pp20) cc_final: 0.5798 (pp20)
REVERT: A  970 MET cc_start: 0.6403 (mmp) cc_final: 0.6074 (mmp)
  outliers start: 13
  outliers final: 6
  residues processed: 118
  average time/residue: 0.2237
  time to fit residues: 37.1904
Evaluate side-chains
  112 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue 1058 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   chunk 106 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1101 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 = 0.4494 r_free = 0.4494 target = 0.217475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.158154 restraints weight = 9538.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3926 rms_B_bonded: 1.80
r_work: 0.3839 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9203  Z= 0.116
  Angle     :  0.504   8.951  12470  Z= 0.265
  Chirality :  0.038   0.165   1436
  Planarity :  0.004   0.056   1574
  Dihedral  :  7.955 122.104   1318
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.70 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1161
  helix:  2.20 (0.19), residues: 754
  sheet: -1.38 (1.37), residues: 17
  loop : -1.87 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 188 
 HIS   0.004   0.001   HIS A1124 
 PHE   0.017   0.001   PHE A1112 
 TYR   0.015   0.001   TYR A 719 
 ARG   0.003   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04155 (  596)
  hydrogen bonds       : angle       3.82607 ( 1764)
  covalent geometry    : bond        0.00233 ( 9203)
  covalent geometry    : angle       0.50429 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.8349 (tp30) cc_final: 0.7872 (tp30)
REVERT: A  173 MET cc_start: 0.7515 (tpp) cc_final: 0.7077 (mmm)
REVERT: A  266 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7651 (mtpt)
REVERT: A  440 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7201 (tpt170)
REVERT: A  478 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7413 (pm20)
REVERT: A  970 MET cc_start: 0.6369 (mmp) cc_final: 0.6048 (mmp)
  outliers start: 10
  outliers final: 8
  residues processed: 119
  average time/residue: 0.2197
  time to fit residues: 36.5579
Evaluate side-chains
  115 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue 1029 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 37 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 762 HIS
** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1101 HIS ** 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 = 0.4473 r_free = 0.4473 target = 0.216896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.165601 restraints weight = 9248.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 2.01
r_work: 0.3756 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3636 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9203  Z= 0.173
  Angle     :  0.572   9.644  12470  Z= 0.300
  Chirality :  0.041   0.158   1436
  Planarity :  0.004   0.049   1574
  Dihedral  :  7.829 111.012   1318
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.49 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.24), residues: 1161
  helix:  1.69 (0.19), residues: 762
  sheet: -1.44 (1.37), residues: 17
  loop : -1.85 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 188 
 HIS   0.008   0.001   HIS A 171 
 PHE   0.022   0.002   PHE A  72 
 TYR   0.016   0.002   TYR A  89 
 ARG   0.004   0.001   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04821 (  596)
  hydrogen bonds       : angle       4.10001 ( 1764)
  covalent geometry    : bond        0.00378 ( 9203)
  covalent geometry    : angle       0.57237 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A  141 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5524 (mp0)
REVERT: A  152 ASN cc_start: 0.6477 (m-40) cc_final: 0.6223 (m-40)
REVERT: A  173 MET cc_start: 0.7448 (tpp) cc_final: 0.7009 (mmm)
REVERT: A  266 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7807 (mtpt)
REVERT: A  440 ARG cc_start: 0.7649 (ttp80) cc_final: 0.7115 (tpt170)
REVERT: A  444 GLN cc_start: 0.7589 (pm20) cc_final: 0.6988 (pm20)
REVERT: A  478 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7365 (pm20)
REVERT: A  481 ARG cc_start: 0.7109 (mmm160) cc_final: 0.6454 (mmm160)
  outliers start: 20
  outliers final: 13
  residues processed: 124
  average time/residue: 0.2094
  time to fit residues: 36.6522
Evaluate side-chains
  126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  692 MET
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue 1058 VAL
Chi-restraints excluded: chain A residue 1116 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 101 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 108 optimal weight:    5.9990
   chunk 33 optimal weight:   20.0000
   chunk 47 optimal weight:   20.0000
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 486 HIS
A 513 GLN
** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.218081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.161356 restraints weight = 9282.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 1.69
r_work: 0.3761 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9203  Z= 0.155
  Angle     :  0.550   9.849  12470  Z= 0.287
  Chirality :  0.040   0.183   1436
  Planarity :  0.004   0.045   1574
  Dihedral  :  7.460 104.615   1318
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.38 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.25), residues: 1161
  helix:  1.67 (0.19), residues: 761
  sheet: -1.61 (1.35), residues: 17
  loop : -1.83 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 188 
 HIS   0.007   0.001   HIS A 171 
 PHE   0.019   0.002   PHE A 552 
 TYR   0.015   0.001   TYR A 286 
 ARG   0.003   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04572 (  596)
  hydrogen bonds       : angle       4.05613 ( 1764)
  covalent geometry    : bond        0.00337 ( 9203)
  covalent geometry    : angle       0.55031 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.966 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.8281 (tp30) cc_final: 0.7813 (tp30)
REVERT: A  141 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5332 (mp0)
REVERT: A  152 ASN cc_start: 0.6492 (m-40) cc_final: 0.6251 (m-40)
REVERT: A  173 MET cc_start: 0.7455 (tpp) cc_final: 0.7011 (mmm)
REVERT: A  266 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7776 (mtpt)
REVERT: A  444 GLN cc_start: 0.7633 (pm20) cc_final: 0.6961 (pm20)
REVERT: A  478 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7309 (pm20)
REVERT: A  696 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6669 (mm-30)
  outliers start: 22
  outliers final: 14
  residues processed: 125
  average time/residue: 0.1955
  time to fit residues: 35.1396
Evaluate side-chains
  124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  692 MET
Chi-restraints excluded: chain A residue  697 TRP
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue 1058 VAL
Chi-restraints excluded: chain A residue 1116 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 103 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   chunk 68 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 80 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 513 GLN
** A 812 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 = 0.4473 r_free = 0.4473 target = 0.216808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.163019 restraints weight = 9239.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.09
r_work: 0.3749 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9203  Z= 0.167
  Angle     :  0.568  10.675  12470  Z= 0.297
  Chirality :  0.040   0.199   1436
  Planarity :  0.004   0.046   1574
  Dihedral  :  7.244  97.663   1318
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.44 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.24), residues: 1161
  helix:  1.57 (0.19), residues: 761
  sheet: -1.77 (1.30), residues: 17
  loop : -1.92 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 188 
 HIS   0.009   0.001   HIS A 486 
 PHE   0.019   0.002   PHE A  72 
 TYR   0.014   0.002   TYR A 286 
 ARG   0.004   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04708 (  596)
  hydrogen bonds       : angle       4.12930 ( 1764)
  covalent geometry    : bond        0.00369 ( 9203)
  covalent geometry    : angle       0.56789 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8266 (m-10) cc_final: 0.7658 (m-10)
REVERT: A  116 GLU cc_start: 0.8329 (tp30) cc_final: 0.7925 (tp30)
REVERT: A  141 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5394 (mp0)
REVERT: A  173 MET cc_start: 0.7455 (tpp) cc_final: 0.7029 (mmm)
REVERT: A  266 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7807 (mtpt)
REVERT: A  444 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.6980 (pm20)
REVERT: A  478 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7309 (pm20)
REVERT: A 1168 LYS cc_start: 0.6468 (ptpp) cc_final: 0.6183 (ptmm)
  outliers start: 27
  outliers final: 17
  residues processed: 127
  average time/residue: 0.1898
  time to fit residues: 34.3965
Evaluate side-chains
  130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  692 MET
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  987 ILE
Chi-restraints excluded: chain A residue 1058 VAL
Chi-restraints excluded: chain A residue 1116 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 55 optimal weight:    0.2980
   chunk 64 optimal weight:    0.4980
   chunk 108 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 114 optimal weight:   30.0000
   chunk 46 optimal weight:    9.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 812 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 = 0.4481 r_free = 0.4481 target = 0.215419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.159408 restraints weight = 9524.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 2.16
r_work: 0.3813 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3694 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
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      :  0.002   0.033   9203  Z= 0.113
  Angle     :  0.540  13.703  12470  Z= 0.273
  Chirality :  0.039   0.207   1436
  Planarity :  0.004   0.046   1574
  Dihedral  :  6.870  93.886   1318
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.70 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.25), residues: 1161
  helix:  2.03 (0.19), residues: 754
  sheet: -2.09 (1.22), residues: 17
  loop : -1.89 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 188 
 HIS   0.007   0.001   HIS A 762 
 PHE   0.017   0.001   PHE A 552 
 TYR   0.012   0.001   TYR A 286 
 ARG   0.002   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04026 (  596)
  hydrogen bonds       : angle       3.87499 ( 1764)
  covalent geometry    : bond        0.00225 ( 9203)
  covalent geometry    : angle       0.54013 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8180 (m-10) cc_final: 0.7595 (m-10)
REVERT: A  116 GLU cc_start: 0.8200 (tp30) cc_final: 0.7802 (tp30)
REVERT: A  141 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5149 (mp0)
REVERT: A  143 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7540 (mtp180)
REVERT: A  173 MET cc_start: 0.7527 (tpp) cc_final: 0.7060 (mmm)
REVERT: A  266 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7792 (mtpt)
REVERT: A  444 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7003 (pm20)
REVERT: A  478 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7385 (pm20)
REVERT: A  481 ARG cc_start: 0.6921 (mmm160) cc_final: 0.6434 (mmm160)
  outliers start: 18
  outliers final: 12
  residues processed: 129
  average time/residue: 0.2229
  time to fit residues: 39.7318
Evaluate side-chains
  123 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  697 TRP
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  821 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9990
   chunk 68 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 112 optimal weight:    0.4980
   chunk 100 optimal weight:    3.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
** A 812 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 = 0.4474 r_free = 0.4474 target = 0.216765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.162388 restraints weight = 9443.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.99
r_work: 0.3731 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3613 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9203  Z= 0.177
  Angle     :  0.616  12.658  12470  Z= 0.312
  Chirality :  0.041   0.198   1436
  Planarity :  0.004   0.046   1574
  Dihedral  :  6.964  79.012   1318
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.70 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1161
  helix:  1.65 (0.19), residues: 762
  sheet: -2.11 (1.22), residues: 17
  loop : -1.94 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 188 
 HIS   0.009   0.001   HIS A 486 
 PHE   0.022   0.002   PHE A  72 
 TYR   0.014   0.002   TYR A  89 
 ARG   0.004   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04694 (  596)
  hydrogen bonds       : angle       4.07729 ( 1764)
  covalent geometry    : bond        0.00392 ( 9203)
  covalent geometry    : angle       0.61644 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8262 (m-10) cc_final: 0.7652 (m-10)
REVERT: A  116 GLU cc_start: 0.8333 (tp30) cc_final: 0.7905 (tp30)
REVERT: A  141 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5333 (mp0)
REVERT: A  173 MET cc_start: 0.7450 (tpp) cc_final: 0.7024 (mmm)
REVERT: A  266 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7805 (mtpt)
REVERT: A  444 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6999 (pm20)
REVERT: A  478 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7303 (pm20)
  outliers start: 24
  outliers final: 17
  residues processed: 126
  average time/residue: 0.2012
  time to fit residues: 35.9678
Evaluate side-chains
  130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  692 MET
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue 1058 VAL
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1216 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 58 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 34 optimal weight:   20.0000
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 812 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 = 0.4510 r_free = 0.4510 target = 0.221037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.165241 restraints weight = 9269.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 1.70
r_work: 0.3804 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3685 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9203  Z= 0.122
  Angle     :  0.575  14.019  12470  Z= 0.286
  Chirality :  0.039   0.218   1436
  Planarity :  0.004   0.047   1574
  Dihedral  :  6.600  69.339   1318
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.55 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.25), residues: 1161
  helix:  1.97 (0.19), residues: 754
  sheet: -2.27 (1.19), residues: 17
  loop : -2.02 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 188 
 HIS   0.007   0.001   HIS A 486 
 PHE   0.016   0.001   PHE A 552 
 TYR   0.013   0.001   TYR A 286 
 ARG   0.003   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04166 (  596)
  hydrogen bonds       : angle       3.91762 ( 1764)
  covalent geometry    : bond        0.00251 ( 9203)
  covalent geometry    : angle       0.57489 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8190 (m-10) cc_final: 0.7531 (m-10)
REVERT: A  116 GLU cc_start: 0.8239 (tp30) cc_final: 0.7798 (tp30)
REVERT: A  141 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5149 (mp0)
REVERT: A  173 MET cc_start: 0.7551 (tpp) cc_final: 0.7066 (mmm)
REVERT: A  266 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7780 (mtpt)
REVERT: A  444 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6966 (pm20)
REVERT: A  478 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7326 (pm20)
  outliers start: 19
  outliers final: 14
  residues processed: 124
  average time/residue: 0.2326
  time to fit residues: 39.8531
Evaluate side-chains
  129 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1216 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 95 optimal weight:   30.0000
   chunk 5 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1101 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.221924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.166150 restraints weight = 9338.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 1.70
r_work: 0.3810 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9203  Z= 0.122
  Angle     :  0.579  13.137  12470  Z= 0.287
  Chirality :  0.039   0.217   1436
  Planarity :  0.004   0.047   1574
  Dihedral  :  6.021  66.104   1318
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 18.34 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.25), residues: 1161
  helix:  2.04 (0.19), residues: 753
  sheet: -2.39 (1.15), residues: 17
  loop : -1.97 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 188 
 HIS   0.007   0.001   HIS A 486 
 PHE   0.025   0.001   PHE A  35 
 TYR   0.012   0.001   TYR A 286 
 ARG   0.009   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04133 (  596)
  hydrogen bonds       : angle       3.88585 ( 1764)
  covalent geometry    : bond        0.00253 ( 9203)
  covalent geometry    : angle       0.57925 (12470)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8193 (m-10) cc_final: 0.7543 (m-10)
REVERT: A  116 GLU cc_start: 0.8236 (tp30) cc_final: 0.7803 (tp30)
REVERT: A  141 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5154 (mp0)
REVERT: A  173 MET cc_start: 0.7537 (tpp) cc_final: 0.7064 (mmm)
REVERT: A  266 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7749 (mtpt)
REVERT: A  444 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6979 (pm20)
REVERT: A  478 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7361 (pm20)
REVERT: A 1177 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7295 (mm)
  outliers start: 18
  outliers final: 14
  residues processed: 126
  average time/residue: 0.2223
  time to fit residues: 39.0615
Evaluate side-chains
  130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue 1058 VAL
Chi-restraints excluded: chain A residue 1098 ILE
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1177 LEU
Chi-restraints excluded: chain A residue 1216 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0170
   chunk 52 optimal weight:    0.7980
   chunk 22 optimal weight:   10.0000
   chunk 94 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1101 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.223272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.168176 restraints weight = 9241.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 1.69
r_work: 0.3831 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9203  Z= 0.116
  Angle     :  0.563  12.100  12470  Z= 0.281
  Chirality :  0.039   0.224   1436
  Planarity :  0.004   0.047   1574
  Dihedral  :  5.728  66.890   1318
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 18.76 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1161
  helix:  2.13 (0.19), residues: 753
  sheet: -2.42 (1.15), residues: 17
  loop : -1.94 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 188 
 HIS   0.007   0.001   HIS A 762 
 PHE   0.024   0.001   PHE A  35 
 TYR   0.011   0.001   TYR A 286 
 ARG   0.006   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04002 (  596)
  hydrogen bonds       : angle       3.82330 ( 1764)
  covalent geometry    : bond        0.00235 ( 9203)
  covalent geometry    : angle       0.56316 (12470)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7867.09 seconds
wall clock time: 135 minutes 44.15 seconds (8144.15 seconds total)