Starting phenix.real_space_refine
on Wed Sep 17 14:05:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9juk_61828/09_2025/9juk_61828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9juk_61828/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9juk_61828/09_2025/9juk_61828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9juk_61828/09_2025/9juk_61828.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9juk_61828/09_2025/9juk_61828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9juk_61828/09_2025/9juk_61828.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.36, per 1000 atoms: 0.26
  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: 0.82
  Conformation dependent library (CDL) restraints added in 302.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.34
  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: 1.49

  Time building geometry restraints manager: 1.06 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:             1.140
  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:          0.170
  Check model and map are aligned:         0.050
  Set scattering table:                    0.010
  Process input model:                     10.110
  Find NCS groups from input model:        0.040
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.810
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.003   0.000   ARG A 481 
 TYR   0.025   0.002   TYR A 908 
 PHE   0.024   0.001   PHE A 552 
 TRP   0.014   0.001   TRP A 791 
 HIS   0.004   0.001   HIS A 762 

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

*********************** 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  : 0.245 
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: 0.1062
  time to fit residues: 18.7807
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  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    0.0010
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    2.3992

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1040 GLN
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 = 0.4488 r_free = 0.4488 target = 0.218389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.160637 restraints weight = 9418.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 1.74
r_work: 0.3749 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.1272

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= 0.196
  Angle     :  0.604   8.467  12470  Z= 0.318
  Chirality :  0.042   0.154   1436
  Planarity :  0.005   0.079   1574
  Dihedral  :  9.424 124.801   1318
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  9.80 %
    Favored  : 88.62 %
  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 aren not related in a simple way.
  whole:  0.70 (0.25), residues: 1161
  helix:  1.61 (0.18), residues: 762
  sheet: -0.90 (1.53), residues: 17
  loop : -1.93 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 777 
 TYR   0.020   0.002   TYR A 908 
 PHE   0.023   0.002   PHE A 552 
 TRP   0.022   0.002   TRP A 188 
 HIS   0.009   0.002   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 9203)
  covalent geometry    : angle       0.60371 (12470)
  hydrogen bonds       : bond        0.05094 (  596)
  hydrogen bonds       : angle       4.27471 ( 1764)

*********************** 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
  131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.8443 (tp30) cc_final: 0.8026 (tp30)
REVERT: A  141 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5407 (mp0)
REVERT: A  440 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7274 (tpt170)
REVERT: A  478 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7445 (pm20)
REVERT: A  760 LEU cc_start: 0.7981 (tp) cc_final: 0.7490 (tt)
  outliers start: 15
  outliers final: 9
  residues processed: 121
  average time/residue: 0.1033
  time to fit residues: 17.4843
Evaluate side-chains
  123 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  359 VAL
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  832 LEU
Chi-restraints excluded: chain A residue 1058 VAL
Chi-restraints excluded: chain A residue 1116 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 75 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 107 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 98 optimal weight:    8.9990
   chunk 101 optimal weight:    0.1980
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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 = 0.4445 r_free = 0.4445 target = 0.213802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.161867 restraints weight = 9342.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.94
r_work: 0.3701 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3579 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9203  Z= 0.215
  Angle     :  0.639   9.893  12470  Z= 0.331
  Chirality :  0.043   0.168   1436
  Planarity :  0.005   0.061   1574
  Dihedral  :  8.537 115.269   1318
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.86 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.24), residues: 1161
  helix:  1.30 (0.18), residues: 763
  sheet: -1.00 (1.50), residues: 17
  loop : -1.99 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 777 
 TYR   0.016   0.002   TYR A 908 
 PHE   0.025   0.002   PHE A 552 
 TRP   0.016   0.002   TRP A 188 
 HIS   0.010   0.002   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 9203)
  covalent geometry    : angle       0.63872 (12470)
  hydrogen bonds       : bond        0.05241 (  596)
  hydrogen bonds       : angle       4.37883 ( 1764)

*********************** 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
  129 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.8480 (tp30) cc_final: 0.8228 (tp30)
REVERT: A  141 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5610 (mp0)
REVERT: A  152 ASN cc_start: 0.6537 (m-40) cc_final: 0.6327 (m-40)
REVERT: A  173 MET cc_start: 0.7455 (tpp) cc_final: 0.6973 (mmm)
REVERT: A  266 LYS cc_start: 0.8261 (mtmm) cc_final: 0.7927 (mtpt)
REVERT: A  760 LEU cc_start: 0.8136 (tp) cc_final: 0.7545 (tt)
REVERT: A 1112 PHE cc_start: 0.7322 (p90) cc_final: 0.6612 (p90)
  outliers start: 21
  outliers final: 15
  residues processed: 118
  average time/residue: 0.0926
  time to fit residues: 15.9089
Evaluate side-chains
  121 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  303 ASN
Chi-restraints excluded: chain A residue  359 VAL
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  768 VAL
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 1098 ILE
Chi-restraints excluded: chain A residue 1116 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 90 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0270
   chunk 65 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.9242

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.212986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.153504 restraints weight = 9540.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.73
r_work: 0.3781 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3665 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9203  Z= 0.124
  Angle     :  0.533  10.232  12470  Z= 0.277
  Chirality :  0.039   0.139   1436
  Planarity :  0.004   0.047   1574
  Dihedral  :  8.031 110.765   1318
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.81 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.25), residues: 1161
  helix:  1.82 (0.19), residues: 758
  sheet: -1.42 (1.41), residues: 17
  loop : -1.91 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 777 
 TYR   0.018   0.001   TYR A 286 
 PHE   0.018   0.001   PHE A 552 
 TRP   0.013   0.001   TRP A 188 
 HIS   0.004   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9203)
  covalent geometry    : angle       0.53346 (12470)
  hydrogen bonds       : bond        0.04316 (  596)
  hydrogen bonds       : angle       4.03718 ( 1764)

*********************** 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
  132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8183 (m-10) cc_final: 0.7579 (m-10)
REVERT: A  141 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5098 (mp0)
REVERT: A  152 ASN cc_start: 0.6469 (m-40) cc_final: 0.6231 (m-40)
REVERT: A  173 MET cc_start: 0.7453 (tpp) cc_final: 0.6996 (mmm)
REVERT: A  266 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7798 (mtpt)
REVERT: A 1112 PHE cc_start: 0.7130 (p90) cc_final: 0.6616 (p90)
  outliers start: 19
  outliers final: 14
  residues processed: 124
  average time/residue: 0.0884
  time to fit residues: 16.0105
Evaluate side-chains
  120 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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  344 ILE
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  697 TRP
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  789 MET
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  987 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 103 optimal weight:   20.0000
   chunk 74 optimal weight:    0.0170
   chunk 108 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    2.4024

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

Flipped N/Q/H residues before XYZ refinement:
A 513 GLN
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4460 r_free = 0.4460 target = 0.215056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.163462 restraints weight = 9315.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 1.85
r_work: 0.3736 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3618 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9203  Z= 0.194
  Angle     :  0.605  10.440  12470  Z= 0.313
  Chirality :  0.041   0.145   1436
  Planarity :  0.004   0.046   1574
  Dihedral  :  7.973 104.309   1318
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.24), residues: 1161
  helix:  1.44 (0.18), residues: 762
  sheet: -1.51 (1.40), residues: 17
  loop : -1.97 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 777 
 TYR   0.015   0.002   TYR A 286 
 PHE   0.022   0.002   PHE A  72 
 TRP   0.012   0.002   TRP A 188 
 HIS   0.009   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 9203)
  covalent geometry    : angle       0.60550 (12470)
  hydrogen bonds       : bond        0.04942 (  596)
  hydrogen bonds       : angle       4.27238 ( 1764)

*********************** 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
  131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   92 TYR cc_start: 0.8285 (m-10) cc_final: 0.7694 (m-10)
REVERT: A  116 GLU cc_start: 0.8346 (tp30) cc_final: 0.7975 (tp30)
REVERT: A  141 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5354 (mp0)
REVERT: A  173 MET cc_start: 0.7411 (tpp) cc_final: 0.6991 (mmm)
REVERT: A  266 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7881 (mtpt)
REVERT: A  273 MET cc_start: 0.7846 (mmm) cc_final: 0.7631 (mmm)
REVERT: A  444 GLN cc_start: 0.7570 (pm20) cc_final: 0.6912 (pm20)
REVERT: A  478 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7286 (pm20)
REVERT: A 1111 LEU cc_start: 0.7469 (mt) cc_final: 0.7191 (mt)
REVERT: A 1112 PHE cc_start: 0.7571 (p90) cc_final: 0.7310 (p90)
  outliers start: 23
  outliers final: 14
  residues processed: 121
  average time/residue: 0.0912
  time to fit residues: 15.9239
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  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  359 VAL
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  987 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 96 optimal weight:    0.4980
   chunk 48 optimal weight:    0.2980
   chunk 55 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 115 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 513 GLN
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4442 r_free = 0.4442 target = 0.210479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.155952 restraints weight = 9576.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.09
r_work: 0.3768 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3648 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.2053

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= 0.140
  Angle     :  0.558  11.590  12470  Z= 0.288
  Chirality :  0.039   0.158   1436
  Planarity :  0.004   0.046   1574
  Dihedral  :  7.564 102.060   1318
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.70 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.25), residues: 1161
  helix:  1.70 (0.19), residues: 758
  sheet: -1.98 (1.27), residues: 17
  loop : -2.05 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 777 
 TYR   0.014   0.001   TYR A 286 
 PHE   0.018   0.001   PHE A  35 
 TRP   0.012   0.001   TRP A 188 
 HIS   0.005   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9203)
  covalent geometry    : angle       0.55825 (12470)
  hydrogen bonds       : bond        0.04468 (  596)
  hydrogen bonds       : angle       4.11427 ( 1764)

*********************** 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
  135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8235 (m-10) cc_final: 0.7575 (m-10)
REVERT: A  116 GLU cc_start: 0.8330 (tp30) cc_final: 0.7952 (tp30)
REVERT: A  141 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5017 (mp0)
REVERT: A  173 MET cc_start: 0.7489 (tpp) cc_final: 0.7041 (mmm)
REVERT: A  266 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7793 (mtpt)
REVERT: A  444 GLN cc_start: 0.7613 (pm20) cc_final: 0.6916 (pm20)
REVERT: A  478 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7332 (pm20)
REVERT: A  766 ASP cc_start: 0.6736 (m-30) cc_final: 0.6436 (m-30)
REVERT: A 1111 LEU cc_start: 0.7365 (mt) cc_final: 0.7104 (mt)
  outliers start: 23
  outliers final: 15
  residues processed: 125
  average time/residue: 0.0848
  time to fit residues: 15.3388
Evaluate side-chains
  123 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
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  303 ASN
Chi-restraints excluded: chain A residue  359 VAL
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  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  987 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 103 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 32 optimal weight:    0.1980
   chunk 90 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.217292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.163286 restraints weight = 9357.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 2.08
r_work: 0.3796 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3673 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9203  Z= 0.150
  Angle     :  0.594  12.995  12470  Z= 0.299
  Chirality :  0.041   0.310   1436
  Planarity :  0.004   0.046   1574
  Dihedral  :  7.424  98.178   1318
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.97 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.24), residues: 1161
  helix:  1.64 (0.19), residues: 761
  sheet: -2.24 (1.21), residues: 17
  loop : -2.02 (0.28), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 777 
 TYR   0.013   0.001   TYR A 286 
 PHE   0.020   0.002   PHE A  35 
 TRP   0.012   0.001   TRP A 188 
 HIS   0.006   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9203)
  covalent geometry    : angle       0.59375 (12470)
  hydrogen bonds       : bond        0.04538 (  596)
  hydrogen bonds       : angle       4.13633 ( 1764)

*********************** 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
  139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8238 (m-10) cc_final: 0.7575 (m-10)
REVERT: A  116 GLU cc_start: 0.8375 (tp30) cc_final: 0.7984 (tp30)
REVERT: A  141 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5049 (mp0)
REVERT: A  173 MET cc_start: 0.7511 (tpp) cc_final: 0.7080 (mmm)
REVERT: A  266 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7769 (mtpt)
REVERT: A  435 LYS cc_start: 0.7521 (tttm) cc_final: 0.7119 (tmtt)
REVERT: A  444 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6906 (pm20)
REVERT: A  478 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7365 (pm20)
REVERT: A  766 ASP cc_start: 0.6804 (m-30) cc_final: 0.6515 (m-30)
REVERT: A 1168 LYS cc_start: 0.6361 (ptpp) cc_final: 0.6055 (ptmm)
  outliers start: 25
  outliers final: 17
  residues processed: 126
  average time/residue: 0.0954
  time to fit residues: 17.1931
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  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  444 GLN
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  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  987 ILE
Chi-restraints excluded: chain A residue 1058 VAL
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1216 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 112 optimal weight:    0.0170
   chunk 91 optimal weight:    8.9990
   chunk 88 optimal weight:    4.9990
   chunk 110 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 107 optimal weight:    9.9990
   overall best weight:    0.9622

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.212967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.156976 restraints weight = 9565.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 2.02
r_work: 0.3820 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3700 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.2179

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= 0.124
  Angle     :  0.564  12.525  12470  Z= 0.284
  Chirality :  0.040   0.282   1436
  Planarity :  0.004   0.046   1574
  Dihedral  :  7.061  93.546   1318
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.07 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.25), residues: 1161
  helix:  1.91 (0.19), residues: 755
  sheet: -2.48 (1.16), residues: 17
  loop : -2.05 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 777 
 TYR   0.011   0.001   TYR A 286 
 PHE   0.019   0.001   PHE A  35 
 TRP   0.011   0.001   TRP A 188 
 HIS   0.005   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9203)
  covalent geometry    : angle       0.56370 (12470)
  hydrogen bonds       : bond        0.04166 (  596)
  hydrogen bonds       : angle       3.98574 ( 1764)

*********************** 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
  137 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8217 (m-10) cc_final: 0.7540 (m-10)
REVERT: A  116 GLU cc_start: 0.8311 (tp30) cc_final: 0.7922 (tp30)
REVERT: A  173 MET cc_start: 0.7585 (tpp) cc_final: 0.7130 (mmm)
REVERT: A  266 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7770 (mtpt)
REVERT: A  444 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6938 (pm20)
REVERT: A  478 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7275 (pm20)
REVERT: A  729 TYR cc_start: 0.6806 (m-80) cc_final: 0.5917 (m-80)
REVERT: A  766 ASP cc_start: 0.6706 (m-30) cc_final: 0.6434 (m-30)
REVERT: A 1168 LYS cc_start: 0.6453 (ptpp) cc_final: 0.6133 (ptmm)
  outliers start: 23
  outliers final: 19
  residues processed: 123
  average time/residue: 0.1047
  time to fit residues: 17.8454
Evaluate side-chains
  131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  522 LEU
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  996 VAL
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 1216 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 92 optimal weight:   20.0000
   chunk 94 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0980
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.4493 r_free = 0.4493 target = 0.218991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.162972 restraints weight = 9357.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 1.68
r_work: 0.3826 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.2248

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= 0.135
  Angle     :  0.583  12.167  12470  Z= 0.292
  Chirality :  0.040   0.270   1436
  Planarity :  0.004   0.046   1574
  Dihedral  :  6.946  90.422   1318
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.76 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1161
  helix:  1.89 (0.19), residues: 755
  sheet: -2.52 (1.15), residues: 17
  loop : -2.03 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 777 
 TYR   0.012   0.001   TYR A 286 
 PHE   0.019   0.001   PHE A  35 
 TRP   0.011   0.001   TRP A 188 
 HIS   0.006   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9203)
  covalent geometry    : angle       0.58300 (12470)
  hydrogen bonds       : bond        0.04313 (  596)
  hydrogen bonds       : angle       3.96878 ( 1764)

*********************** 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
  133 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8199 (m-10) cc_final: 0.7524 (m-10)
REVERT: A  116 GLU cc_start: 0.8304 (tp30) cc_final: 0.7881 (tp30)
REVERT: A  141 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5254 (mp0)
REVERT: A  173 MET cc_start: 0.7472 (tpp) cc_final: 0.7029 (mmm)
REVERT: A  266 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7736 (mtpt)
REVERT: A  444 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.6937 (pm20)
REVERT: A  478 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7217 (pm20)
REVERT: A  729 TYR cc_start: 0.6806 (m-80) cc_final: 0.5869 (m-80)
REVERT: A  764 PHE cc_start: 0.7153 (m-80) cc_final: 0.6812 (m-80)
REVERT: A 1168 LYS cc_start: 0.6505 (ptpp) cc_final: 0.6164 (ptmm)
  outliers start: 24
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1000
  time to fit residues: 16.7178
Evaluate side-chains
  126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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  303 ASN
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  522 LEU
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  996 VAL
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 1216 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 92 optimal weight:    8.9990
   chunk 69 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.4460 r_free = 0.4460 target = 0.212579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.156669 restraints weight = 9526.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.10
r_work: 0.3782 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3662 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9203  Z= 0.130
  Angle     :  0.573  11.843  12470  Z= 0.289
  Chirality :  0.040   0.258   1436
  Planarity :  0.004   0.047   1574
  Dihedral  :  6.780  87.032   1318
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.55 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.25), residues: 1161
  helix:  1.93 (0.19), residues: 754
  sheet: -2.54 (1.14), residues: 17
  loop : -1.99 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1002 
 TYR   0.012   0.001   TYR A 286 
 PHE   0.024   0.001   PHE A  35 
 TRP   0.022   0.001   TRP A 791 
 HIS   0.005   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9203)
  covalent geometry    : angle       0.57273 (12470)
  hydrogen bonds       : bond        0.04235 (  596)
  hydrogen bonds       : angle       3.94668 ( 1764)

********************** 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
  133 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8229 (m-10) cc_final: 0.7578 (m-10)
REVERT: A  116 GLU cc_start: 0.8290 (tp30) cc_final: 0.7855 (tp30)
REVERT: A  141 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5242 (mp0)
REVERT: A  173 MET cc_start: 0.7476 (tpp) cc_final: 0.7019 (mmm)
REVERT: A  266 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7780 (mtpt)
REVERT: A  444 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.6952 (pm20)
REVERT: A  478 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7254 (pm20)
REVERT: A  729 TYR cc_start: 0.6816 (m-80) cc_final: 0.5905 (m-80)
REVERT: A 1168 LYS cc_start: 0.6450 (ptpp) cc_final: 0.6163 (ptmm)
  outliers start: 25
  outliers final: 18
  residues processed: 121
  average time/residue: 0.0975
  time to fit residues: 16.6707
Evaluate side-chains
  126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  522 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  996 VAL
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 1216 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 48 optimal weight:    0.0980
   chunk 31 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 1 optimal weight:    0.3980
   chunk 108 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 54 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.5784

-------------------------------------------------------------------------------
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**
A1040 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.223093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.168229 restraints weight = 9213.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 1.68
r_work: 0.3835 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9203  Z= 0.114
  Angle     :  0.563  11.800  12470  Z= 0.280
  Chirality :  0.039   0.301   1436
  Planarity :  0.004   0.047   1574
  Dihedral  :  6.383  81.052   1318
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.28 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.25), residues: 1161
  helix:  2.12 (0.19), residues: 753
  sheet: -2.60 (1.11), residues: 17
  loop : -1.94 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1002 
 TYR   0.011   0.001   TYR A 286 
 PHE   0.024   0.001   PHE A  35 
 TRP   0.016   0.001   TRP A 791 
 HIS   0.005   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 9203)
  covalent geometry    : angle       0.56293 (12470)
  hydrogen bonds       : bond        0.03954 (  596)
  hydrogen bonds       : angle       3.82830 ( 1764)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3897.67 seconds
wall clock time: 67 minutes 4.99 seconds (4024.99 seconds total)