Starting phenix.real_space_refine
on Wed Sep 17 14:24:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jum_61830/09_2025/9jum_61830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jum_61830/09_2025/9jum_61830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jum_61830/09_2025/9jum_61830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jum_61830/09_2025/9jum_61830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jum_61830/09_2025/9jum_61830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jum_61830/09_2025/9jum_61830.cif"
  }
  resolution = 3.1
  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=   0.002
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    5784      2.51       5
     N    1555      2.21       5
     O    1681      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 9069
  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: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 98
          Unusual residues: {' MG': 2, 'ANP': 2, 'BLD': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 1.91, per 1000 atoms: 0.21
  Number of scatterers: 9069
  At special positions: 0
  Unit cell: (106.02, 98.58, 129.27, 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    1681      8.00
     N    1555      7.00
     C    5784      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: 0.77
  Conformation dependent library (CDL) restraints added in 310.6 milliseconds
  
  Enol-peptide restraints added in 476.8 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:
      41 helices and 3 sheets defined
      70.0% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 34
    Processing helix  chain 'A' and resid 37 through 75
      Proline residue:  A  59  - end of helix
      removed outlier: 4.048A  pdb=" N   LEU A  62 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 132
      removed outlier: 3.701A  pdb=" N   LYS A 121 " --> pdb=" O   ARG A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 141
    Processing helix  chain 'A' and resid 143 through 187
      removed outlier: 4.440A  pdb=" N   ALA A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LYS A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   LEU A 166 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   GLY A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
    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
    Processing helix  chain 'A' and resid 245 through 299
    Processing helix  chain 'A' and resid 303 through 347
      Proline residue:  A 326  - end of helix
    Processing helix  chain 'A' and resid 408 through 418
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 459 through 468
    Processing helix  chain 'A' and resid 472 through 480
    Processing helix  chain 'A' and resid 499 through 504
      removed outlier: 4.153A  pdb=" N   ARG A 503 " --> pdb=" O   GLN A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 523
    Processing helix  chain 'A' and resid 538 through 552
    Processing helix  chain 'A' and resid 564 through 571
      removed outlier: 4.030A  pdb=" N   ILE A 568 " --> pdb=" O   ARG A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
    Processing helix  chain 'A' and resid 696 through 729
      removed outlier: 3.649A  pdb=" N   TYR A 729 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 787
      removed outlier: 4.140A  pdb=" N   SER A 752 " --> pdb=" O   ILE A 748 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ALA A 753 " --> pdb=" O   GLY A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 793
    Processing helix  chain 'A' and resid 798 through 869
      removed outlier: 4.303A  pdb=" N   ARG A 820 " --> pdb=" O   ALA A 816 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR A 828 " --> pdb=" O   ILE A 824 " (cutoff:3.500A)
      removed outlier: 8.636A  pdb=" N   ARG A 844 " --> pdb=" O   VAL A 840 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   LEU A 845 " --> pdb=" O   LEU A 841 " (cutoff:3.500A)
      Proline residue:  A 854  - end of helix
    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 898
    Processing helix  chain 'A' and resid 900 through 954
      Proline residue:  A 914  - end of helix
    Processing helix  chain 'A' and resid 958 through 978
    Processing helix  chain 'A' and resid 979 through 982
    Processing helix  chain 'A' and resid 985 through 1002
      removed outlier: 4.276A  pdb=" N   GLN A 991 " --> pdb=" O   ILE A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1064 through 1073
    Processing helix  chain 'A' and resid 1094 through 1101
    Processing helix  chain 'A' and resid 1115 through 1122
    Processing helix  chain 'A' and resid 1129 through 1139
    Processing helix  chain 'A' and resid 1141 through 1148
    Processing helix  chain 'A' and resid 1150 through 1154
      removed outlier: 3.507A  pdb=" N   LYS A1153 " --> pdb=" O   GLU A1150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1180
      removed outlier: 3.575A  pdb=" N   LYS A1180 " --> pdb=" O   ALA A1176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1191
    Processing helix  chain 'A' and resid 1194 through 1211
    Processing helix  chain 'A' and resid 1234 through 1237
    Processing helix  chain 'A' and resid 1243 through 1250
    Processing helix  chain 'A' and resid 1254 through 1264
    Processing sheet with id=AA1, first strand: chain 'A' and resid 558 through 559
      removed outlier: 3.862A  pdb=" N   ALA A 575 " --> pdb=" O   ALA A 400 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1025 through 1027
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1102 through 1105
      removed outlier: 7.072A  pdb=" N   ALA A1103 " --> pdb=" O   LEU A1185 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   MET A1184 " --> pdb=" O   ILE A1215 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   VAL A1217 " --> pdb=" O   MET A1184 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LEU A1186 " --> pdb=" O   VAL A1217 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL A1229 " --> pdb=" O   THR A1054 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL A1058 " --> pdb=" O   ALA A1231 " (cutoff:3.500A)

    639 hydrogen bonds defined for protein.
    1884 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: 1.71

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1647
        1.33 -     1.45: 2256
        1.45 -     1.57: 5259
        1.57 -     1.69: 10
        1.69 -     1.81: 68
  Bond restraints: 9240
  Sorted by residual:
  bond pdb=" N3B ANP A1304 "
       pdb=" PG  ANP A1304 "
    ideal  model  delta    sigma   weight residual
    1.795  1.632  0.163 2.00e-02 2.50e+03 6.66e+01
  bond pdb=" N3B ANP A1303 "
       pdb=" PG  ANP A1303 "
    ideal  model  delta    sigma   weight residual
    1.795  1.635  0.160 2.00e-02 2.50e+03 6.40e+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 2.42e+01
  bond pdb=" O3A ANP A1304 "
       pdb=" PB  ANP A1304 "
    ideal  model  delta    sigma   weight residual
    1.700  1.604  0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" N   HIS A1251 "
       pdb=" CA  HIS A1251 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 7.40e-03 1.83e+04 1.81e+01
  ... (remaining 9235 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 12192
        2.08 -     4.16: 284
        4.16 -     6.25: 40
        6.25 -     8.33: 8
        8.33 -    10.41: 5
  Bond angle restraints: 12529
  Sorted by residual:
  angle pdb=" CA  GLY A1254 "
        pdb=" C   GLY A1254 "
        pdb=" O   GLY A1254 "
      ideal   model   delta    sigma   weight residual
     122.22  118.24    3.98 6.50e-01 2.37e+00 3.74e+01
  angle pdb=" N3B ANP A1303 "
        pdb=" PG  ANP A1303 "
        pdb=" O2G ANP A1303 "
      ideal   model   delta    sigma   weight residual
     101.05  111.46  -10.41 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" N   LYS A 262 "
        pdb=" CA  LYS A 262 "
        pdb=" C   LYS A 262 "
      ideal   model   delta    sigma   weight residual
     111.28  107.54    3.74 1.09e+00 8.42e-01 1.18e+01
  angle pdb=" CG  ARG A1019 "
        pdb=" CD  ARG A1019 "
        pdb=" NE  ARG A1019 "
      ideal   model   delta    sigma   weight residual
     112.00  119.37   -7.37 2.20e+00 2.07e-01 1.12e+01
  angle pdb=" C   ASP A1253 "
        pdb=" CA  ASP A1253 "
        pdb=" CB  ASP A1253 "
      ideal   model   delta    sigma   weight residual
     116.63  112.94    3.69 1.16e+00 7.43e-01 1.01e+01
  ... (remaining 12524 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.05: 5422
       31.05 -    62.11: 149
       62.11 -    93.16: 39
       93.16 -   124.21: 0
      124.21 -   155.27: 2
  Dihedral angle restraints: 5612
    sinusoidal: 2258
      harmonic: 3354
  Sorted by residual:
  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 -169.58 -155.27     1      3.00e+01 1.11e-03 2.04e+01
  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  -55.72  138.83     1      3.00e+01 1.11e-03 1.87e+01
  dihedral pdb=" CA  ASP A1194 "
           pdb=" C   ASP A1194 "
           pdb=" N   ALA A1195 "
           pdb=" CA  ALA A1195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.75  -17.25     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 5609 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1287
       0.067 -    0.135: 136
       0.135 -    0.202: 19
       0.202 -    0.269: 4
       0.269 -    0.336: 3
  Chirality restraints: 1449
  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   -2.69    0.34 2.00e-01 2.50e+01 2.83e+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   -2.68    0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" C10 BLD A1305 "
            pdb=" C01 BLD A1305 "
            pdb=" C05 BLD A1305 "
            pdb=" C09 BLD A1305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -3.02   -2.70   -0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 1446 not shown)

  Planarity restraints: 1575
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  58 "    0.038 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO A  59 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A  59 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  59 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1021 "   -0.184 9.50e-02 1.11e+02   8.26e-02 4.46e+00
        pdb=" NE  ARG A1021 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1021 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1021 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1021 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 706 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.93e+00
        pdb=" C   GLY A 706 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   GLY A 706 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER A 707 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1572 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 53
        2.52 -     3.11: 7758
        3.11 -     3.71: 15462
        3.71 -     4.30: 20744
        4.30 -     4.90: 33499
  Nonbonded interactions: 77516
  Sorted by model distance:
  nonbonded pdb="MG    MG A1302 "
            pdb=" O1A ANP A1304 "
     model   vdw
     1.922 2.170
  nonbonded pdb=" OG  SER A 410 "
            pdb="MG    MG A1301 "
     model   vdw
     1.992 2.170
  nonbonded pdb=" N   SER A1066 "
            pdb="MG    MG A1302 "
     model   vdw
     2.138 2.250
  nonbonded pdb=" NZ  LYS A 409 "
            pdb="MG    MG A1301 "
     model   vdw
     2.186 2.250
  nonbonded pdb=" O   TRP A 791 "
            pdb=" ND2 ASN A 797 "
     model   vdw
     2.226 3.120
  ... (remaining 77511 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:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.350
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
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      :  0.005   0.163   9240  Z= 0.296
  Angle     :  0.759  10.409  12529  Z= 0.434
  Chirality :  0.048   0.336   1449
  Planarity :  0.006   0.083   1575
  Dihedral  : 15.660 155.266   3454
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  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:  1.53 (0.19), residues: 771
  sheet: -1.76 (1.01), residues: 31
  loop : -1.40 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1050 
 TYR   0.021   0.002   TYR A 286 
 PHE   0.019   0.001   PHE A1144 
 TRP   0.011   0.001   TRP A 441 
 HIS   0.006   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 9240)
  covalent geometry    : angle       0.75915 (12529)
  hydrogen bonds       : bond        0.12780 (  639)
  hydrogen bonds       : angle       5.75747 ( 1884)

*********************** 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
  154 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.8911 (mtp) cc_final: 0.8562 (mtp)
REVERT: A  421 ASP cc_start: 0.8559 (t70) cc_final: 0.8317 (t0)
REVERT: A  437 LEU cc_start: 0.9491 (pt) cc_final: 0.9162 (pp)
REVERT: A  488 PHE cc_start: 0.8442 (t80) cc_final: 0.8140 (t80)
REVERT: A  796 GLU cc_start: 0.8090 (tp30) cc_final: 0.7890 (tp30)
REVERT: A  994 ARG cc_start: 0.8555 (ppt170) cc_final: 0.8272 (tmm-80)
REVERT: A 1007 GLU cc_start: 0.8412 (mp0) cc_final: 0.8195 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1046
  time to fit residues: 22.2173
Evaluate side-chains
  123 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 827 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.107679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.070498 restraints weight = 21936.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 3.07
r_work: 0.2969 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9240  Z= 0.214
  Angle     :  0.647   8.223  12529  Z= 0.340
  Chirality :  0.043   0.172   1449
  Planarity :  0.005   0.061   1575
  Dihedral  : 10.368 150.937   1403
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.69 %
    Favored  : 88.83 %
  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:  1.19 (0.25), residues: 1161
  helix:  1.86 (0.18), residues: 779
  sheet: -1.40 (1.05), residues: 29
  loop : -1.52 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1074 
 TYR   0.023   0.002   TYR A1122 
 PHE   0.023   0.002   PHE A  72 
 TRP   0.014   0.001   TRP A 950 
 HIS   0.009   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 9240)
  covalent geometry    : angle       0.64675 (12529)
  hydrogen bonds       : bond        0.06164 (  639)
  hydrogen bonds       : angle       4.73190 ( 1884)

*********************** 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
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.9092 (mtp) cc_final: 0.8646 (mtp)
REVERT: A  421 ASP cc_start: 0.8784 (t70) cc_final: 0.8564 (t0)
REVERT: A  488 PHE cc_start: 0.8440 (t80) cc_final: 0.8157 (t80)
REVERT: A  507 LEU cc_start: 0.8393 (mm) cc_final: 0.8043 (mm)
REVERT: A  531 ASP cc_start: 0.7264 (t0) cc_final: 0.6882 (t70)
REVERT: A  796 GLU cc_start: 0.8342 (tp30) cc_final: 0.8026 (tp30)
REVERT: A  994 ARG cc_start: 0.8785 (ppt170) cc_final: 0.8523 (tmm-80)
REVERT: A 1048 ARG cc_start: 0.8707 (mmm-85) cc_final: 0.8441 (mmm-85)
REVERT: A 1075 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8467 (m-80)
REVERT: A 1122 TYR cc_start: 0.9155 (t80) cc_final: 0.8926 (t80)
REVERT: A 1134 GLN cc_start: 0.9084 (mt0) cc_final: 0.8722 (mp10)
  outliers start: 14
  outliers final: 10
  residues processed: 136
  average time/residue: 0.1014
  time to fit residues: 19.3873
Evaluate side-chains
  130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  273 MET
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue 1038 ASP
Chi-restraints excluded: chain A residue 1075 PHE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1259 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 50 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0970
   chunk 71 optimal weight:    0.5980
   chunk 2 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.0780

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

Flipped N/Q/H residues before XYZ refinement:
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 827 ASN
A 878 HIS
A1073 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.109693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.072841 restraints weight = 21694.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 3.04
r_work: 0.3018 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9240  Z= 0.141
  Angle     :  0.580   9.188  12529  Z= 0.299
  Chirality :  0.040   0.161   1449
  Planarity :  0.004   0.055   1575
  Dihedral  :  8.828 152.648   1403
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.07 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.51 (0.25), residues: 1161
  helix:  2.11 (0.18), residues: 782
  sheet: -0.74 (1.17), residues: 24
  loop : -1.49 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1050 
 TYR   0.015   0.001   TYR A1122 
 PHE   0.013   0.001   PHE A 757 
 TRP   0.012   0.001   TRP A 950 
 HIS   0.004   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9240)
  covalent geometry    : angle       0.58047 (12529)
  hydrogen bonds       : bond        0.05480 (  639)
  hydrogen bonds       : angle       4.44945 ( 1884)

*********************** 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
  152 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.8930 (mtp) cc_final: 0.8393 (mtm)
REVERT: A  384 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8381 (tttm)
REVERT: A  421 ASP cc_start: 0.8740 (t70) cc_final: 0.8511 (t0)
REVERT: A  488 PHE cc_start: 0.8440 (t80) cc_final: 0.8182 (t80)
REVERT: A  531 ASP cc_start: 0.7215 (t0) cc_final: 0.6899 (t70)
REVERT: A  796 GLU cc_start: 0.8247 (tp30) cc_final: 0.7952 (tp30)
REVERT: A  994 ARG cc_start: 0.8746 (ppt170) cc_final: 0.8463 (tmm-80)
REVERT: A 1075 PHE cc_start: 0.8893 (t80) cc_final: 0.8553 (m-80)
REVERT: A 1129 GLU cc_start: 0.8826 (tp30) cc_final: 0.8606 (tp30)
  outliers start: 14
  outliers final: 9
  residues processed: 143
  average time/residue: 0.0944
  time to fit residues: 19.1311
Evaluate side-chains
  132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  273 MET
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue 1038 ASP
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1206 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 95 optimal weight:   30.0000
   chunk 22 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 96 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 53 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 827 ASN
** A1028 HIS ** 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 = 0.3786 r_free = 0.3786 target = 0.105477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.069376 restraints weight = 22185.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.95
r_work: 0.2923 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9240  Z= 0.272
  Angle     :  0.676   9.958  12529  Z= 0.353
  Chirality :  0.043   0.182   1449
  Planarity :  0.005   0.065   1575
  Dihedral  :  8.572 147.537   1403
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.81 %
    Favored  : 81.56 %
  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:  1.26 (0.25), residues: 1161
  helix:  1.92 (0.18), residues: 777
  sheet: -0.83 (1.18), residues: 24
  loop : -1.54 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 519 
 TYR   0.029   0.002   TYR A1122 
 PHE   0.024   0.002   PHE A  72 
 TRP   0.011   0.001   TRP A 950 
 HIS   0.009   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 9240)
  covalent geometry    : angle       0.67621 (12529)
  hydrogen bonds       : bond        0.06343 (  639)
  hydrogen bonds       : angle       4.69576 ( 1884)

*********************** 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
  161 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 ASP cc_start: 0.8790 (t70) cc_final: 0.8587 (t0)
REVERT: A  488 PHE cc_start: 0.8470 (t80) cc_final: 0.8224 (t80)
REVERT: A  531 ASP cc_start: 0.7220 (t0) cc_final: 0.6870 (t70)
REVERT: A  796 GLU cc_start: 0.8276 (tp30) cc_final: 0.7955 (tp30)
REVERT: A  994 ARG cc_start: 0.8745 (ppt170) cc_final: 0.8496 (tmm-80)
REVERT: A 1117 TYR cc_start: 0.8604 (t80) cc_final: 0.8351 (t80)
REVERT: A 1122 TYR cc_start: 0.9095 (t80) cc_final: 0.8891 (t80)
REVERT: A 1129 GLU cc_start: 0.8832 (tp30) cc_final: 0.8560 (tp30)
  outliers start: 25
  outliers final: 17
  residues processed: 145
  average time/residue: 0.0889
  time to fit residues: 18.2615
Evaluate side-chains
  144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  273 MET
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue 1038 ASP
Chi-restraints excluded: chain A residue 1069 ILE
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1206 ASP
Chi-restraints excluded: chain A residue 1223 THR
Chi-restraints excluded: chain A residue 1259 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 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 = 0.3833 r_free = 0.3833 target = 0.108390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.071670 restraints weight = 21756.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 3.03
r_work: 0.2989 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9240  Z= 0.140
  Angle     :  0.607   9.829  12529  Z= 0.306
  Chirality :  0.041   0.196   1449
  Planarity :  0.004   0.054   1575
  Dihedral  :  8.192 142.440   1403
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.91 %
    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:  1.52 (0.25), residues: 1161
  helix:  2.14 (0.18), residues: 782
  sheet: -1.01 (1.12), residues: 24
  loop : -1.54 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1050 
 TYR   0.022   0.001   TYR A1122 
 PHE   0.012   0.001   PHE A 757 
 TRP   0.010   0.001   TRP A 950 
 HIS   0.003   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9240)
  covalent geometry    : angle       0.60709 (12529)
  hydrogen bonds       : bond        0.05506 (  639)
  hydrogen bonds       : angle       4.45276 ( 1884)

*********************** 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
  150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.9170 (mtm) cc_final: 0.8829 (mtp)
REVERT: A  389 PHE cc_start: 0.9175 (t80) cc_final: 0.8878 (t80)
REVERT: A  488 PHE cc_start: 0.8450 (t80) cc_final: 0.8221 (t80)
REVERT: A  531 ASP cc_start: 0.7330 (t0) cc_final: 0.6957 (t70)
REVERT: A  796 GLU cc_start: 0.8155 (tp30) cc_final: 0.7822 (tp30)
REVERT: A  994 ARG cc_start: 0.8733 (ppt170) cc_final: 0.8455 (tmm-80)
REVERT: A 1117 TYR cc_start: 0.8586 (t80) cc_final: 0.8329 (t80)
REVERT: A 1122 TYR cc_start: 0.8976 (t80) cc_final: 0.8746 (t80)
REVERT: A 1129 GLU cc_start: 0.8886 (tp30) cc_final: 0.8628 (tp30)
  outliers start: 21
  outliers final: 13
  residues processed: 137
  average time/residue: 0.0910
  time to fit residues: 17.5535
Evaluate side-chains
  137 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  273 MET
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue 1038 ASP
Chi-restraints excluded: chain A residue 1065 LYS
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1088 LYS
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1206 ASP
Chi-restraints excluded: chain A residue 1223 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 45 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 70 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 92 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 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 = 0.3810 r_free = 0.3810 target = 0.106813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.069761 restraints weight = 21905.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 3.05
r_work: 0.2955 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9240  Z= 0.184
  Angle     :  0.620  10.310  12529  Z= 0.317
  Chirality :  0.042   0.173   1449
  Planarity :  0.004   0.058   1575
  Dihedral  :  8.075 138.103   1403
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.12 %
    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:  1.57 (0.25), residues: 1161
  helix:  2.18 (0.18), residues: 776
  sheet: -1.05 (0.95), residues: 32
  loop : -1.44 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 556 
 TYR   0.020   0.002   TYR A1122 
 PHE   0.015   0.001   PHE A  72 
 TRP   0.010   0.001   TRP A 950 
 HIS   0.005   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 9240)
  covalent geometry    : angle       0.62018 (12529)
  hydrogen bonds       : bond        0.05692 (  639)
  hydrogen bonds       : angle       4.50412 ( 1884)

*********************** 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
  156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 GLN cc_start: 0.8668 (mm110) cc_final: 0.8453 (mm110)
REVERT: A  241 MET cc_start: 0.9217 (mtm) cc_final: 0.8836 (mtp)
REVERT: A  389 PHE cc_start: 0.9181 (t80) cc_final: 0.8925 (t80)
REVERT: A  488 PHE cc_start: 0.8503 (t80) cc_final: 0.8288 (t80)
REVERT: A  531 ASP cc_start: 0.7413 (t0) cc_final: 0.6986 (t70)
REVERT: A  796 GLU cc_start: 0.8224 (tp30) cc_final: 0.7849 (tp30)
REVERT: A  994 ARG cc_start: 0.8738 (ppt170) cc_final: 0.8466 (tmm-80)
REVERT: A 1117 TYR cc_start: 0.8613 (t80) cc_final: 0.8333 (t80)
REVERT: A 1122 TYR cc_start: 0.9090 (t80) cc_final: 0.8845 (t80)
REVERT: A 1129 GLU cc_start: 0.8883 (tp30) cc_final: 0.8563 (tp30)
  outliers start: 29
  outliers final: 19
  residues processed: 146
  average time/residue: 0.0995
  time to fit residues: 20.4262
Evaluate side-chains
  144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  273 MET
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1038 ASP
Chi-restraints excluded: chain A residue 1065 LYS
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1193 LEU
Chi-restraints excluded: chain A residue 1213 THR
Chi-restraints excluded: chain A residue 1223 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 47 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0770
   chunk 74 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.1142

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

Flipped N/Q/H residues before XYZ refinement:
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 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 = 0.3839 r_free = 0.3839 target = 0.108651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.071944 restraints weight = 21901.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 3.06
r_work: 0.2997 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9240  Z= 0.138
  Angle     :  0.610  10.839  12529  Z= 0.306
  Chirality :  0.041   0.175   1449
  Planarity :  0.004   0.052   1575
  Dihedral  :  7.887 132.923   1403
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  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:  1.64 (0.25), residues: 1161
  helix:  2.25 (0.18), residues: 776
  sheet: -1.03 (0.95), residues: 32
  loop : -1.46 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1050 
 TYR   0.019   0.001   TYR A1122 
 PHE   0.011   0.001   PHE A 853 
 TRP   0.010   0.001   TRP A 950 
 HIS   0.003   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9240)
  covalent geometry    : angle       0.60978 (12529)
  hydrogen bonds       : bond        0.05290 (  639)
  hydrogen bonds       : angle       4.43119 ( 1884)

*********************** 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
  155 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 GLN cc_start: 0.8673 (mm110) cc_final: 0.8459 (mm110)
REVERT: A  229 ILE cc_start: 0.8490 (mp) cc_final: 0.8240 (mp)
REVERT: A  241 MET cc_start: 0.9120 (mtm) cc_final: 0.8902 (mtp)
REVERT: A  369 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7362 (mp0)
REVERT: A  389 PHE cc_start: 0.9220 (t80) cc_final: 0.8966 (t80)
REVERT: A  488 PHE cc_start: 0.8498 (t80) cc_final: 0.8287 (t80)
REVERT: A  531 ASP cc_start: 0.7401 (t0) cc_final: 0.6994 (t70)
REVERT: A  796 GLU cc_start: 0.8244 (tp30) cc_final: 0.7879 (tp30)
REVERT: A  994 ARG cc_start: 0.8688 (ppt170) cc_final: 0.8426 (tmm-80)
REVERT: A 1050 ARG cc_start: 0.9070 (mmt90) cc_final: 0.8727 (mmm160)
REVERT: A 1117 TYR cc_start: 0.8626 (t80) cc_final: 0.8308 (t80)
REVERT: A 1118 GLU cc_start: 0.8851 (pt0) cc_final: 0.8602 (pp20)
REVERT: A 1122 TYR cc_start: 0.9060 (t80) cc_final: 0.8777 (t80)
REVERT: A 1129 GLU cc_start: 0.8881 (tp30) cc_final: 0.8583 (tp30)
  outliers start: 25
  outliers final: 17
  residues processed: 144
  average time/residue: 0.0965
  time to fit residues: 19.6050
Evaluate side-chains
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  273 MET
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1038 ASP
Chi-restraints excluded: chain A residue 1065 LYS
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1193 LEU
Chi-restraints excluded: chain A residue 1223 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0060
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 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 = 0.3865 r_free = 0.3865 target = 0.110059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.074441 restraints weight = 21808.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.99
r_work: 0.3044 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9240  Z= 0.127
  Angle     :  0.600  11.421  12529  Z= 0.298
  Chirality :  0.041   0.225   1449
  Planarity :  0.004   0.050   1575
  Dihedral  :  7.680 129.155   1403
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.49 %
    Favored  : 78.19 %
  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:  1.74 (0.25), residues: 1161
  helix:  2.33 (0.18), residues: 776
  sheet: -0.99 (0.94), residues: 32
  loop : -1.42 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1050 
 TYR   0.020   0.001   TYR A1122 
 PHE   0.012   0.001   PHE A 853 
 TRP   0.011   0.001   TRP A 950 
 HIS   0.003   0.001   HIS A 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9240)
  covalent geometry    : angle       0.59961 (12529)
  hydrogen bonds       : bond        0.04900 (  639)
  hydrogen bonds       : angle       4.36046 ( 1884)

*********************** 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
  161 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 GLN cc_start: 0.8618 (mm110) cc_final: 0.8400 (mm110)
REVERT: A  229 ILE cc_start: 0.8383 (mp) cc_final: 0.8147 (mp)
REVERT: A  241 MET cc_start: 0.9082 (mtm) cc_final: 0.8774 (mtp)
REVERT: A  389 PHE cc_start: 0.9213 (t80) cc_final: 0.8941 (t80)
REVERT: A  488 PHE cc_start: 0.8472 (t80) cc_final: 0.8262 (t80)
REVERT: A  531 ASP cc_start: 0.7337 (t0) cc_final: 0.7017 (t70)
REVERT: A  796 GLU cc_start: 0.8187 (tp30) cc_final: 0.7818 (tp30)
REVERT: A  994 ARG cc_start: 0.8657 (ppt170) cc_final: 0.8384 (tmm-80)
REVERT: A 1043 ARG cc_start: 0.8056 (mmt180) cc_final: 0.7809 (mmp80)
REVERT: A 1117 TYR cc_start: 0.8630 (t80) cc_final: 0.8327 (t80)
REVERT: A 1118 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8621 (pp20)
REVERT: A 1122 TYR cc_start: 0.9063 (t80) cc_final: 0.8754 (t80)
REVERT: A 1129 GLU cc_start: 0.8838 (tp30) cc_final: 0.8581 (tp30)
  outliers start: 22
  outliers final: 15
  residues processed: 150
  average time/residue: 0.0970
  time to fit residues: 20.3793
Evaluate side-chains
  145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1028 HIS
Chi-restraints excluded: chain A residue 1038 ASP
Chi-restraints excluded: chain A residue 1065 LYS
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1193 LEU
Chi-restraints excluded: chain A residue 1223 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   chunk 77 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 112 optimal weight:   20.0000
   chunk 90 optimal weight:    7.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 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 = 0.3825 r_free = 0.3825 target = 0.107670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071749 restraints weight = 21743.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.98
r_work: 0.2984 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9240  Z= 0.165
  Angle     :  0.632  12.343  12529  Z= 0.316
  Chirality :  0.042   0.216   1449
  Planarity :  0.004   0.057   1575
  Dihedral  :  7.748 126.223   1403
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.70 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.25), residues: 1161
  helix:  2.25 (0.18), residues: 775
  sheet: -1.09 (0.95), residues: 32
  loop : -1.36 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 519 
 TYR   0.019   0.002   TYR A1122 
 PHE   0.014   0.001   PHE A  72 
 TRP   0.009   0.001   TRP A 950 
 HIS   0.005   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9240)
  covalent geometry    : angle       0.63211 (12529)
  hydrogen bonds       : bond        0.05341 (  639)
  hydrogen bonds       : angle       4.44042 ( 1884)

*********************** 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
  158 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 GLN cc_start: 0.8634 (mm110) cc_final: 0.8411 (mm110)
REVERT: A  229 ILE cc_start: 0.8398 (mp) cc_final: 0.8171 (mp)
REVERT: A  241 MET cc_start: 0.9241 (mtm) cc_final: 0.8882 (mtp)
REVERT: A  389 PHE cc_start: 0.9271 (t80) cc_final: 0.9001 (t80)
REVERT: A  488 PHE cc_start: 0.8510 (t80) cc_final: 0.8303 (t80)
REVERT: A  531 ASP cc_start: 0.7371 (t0) cc_final: 0.7036 (t70)
REVERT: A  796 GLU cc_start: 0.8149 (tp30) cc_final: 0.7795 (tp30)
REVERT: A  867 MET cc_start: 0.7362 (tpt) cc_final: 0.7160 (tpt)
REVERT: A  994 ARG cc_start: 0.8667 (ppt170) cc_final: 0.8394 (tmm-80)
REVERT: A 1117 TYR cc_start: 0.8640 (t80) cc_final: 0.8327 (t80)
REVERT: A 1118 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8604 (pp20)
REVERT: A 1122 TYR cc_start: 0.9145 (t80) cc_final: 0.8820 (t80)
REVERT: A 1129 GLU cc_start: 0.8876 (tp30) cc_final: 0.8562 (tp30)
  outliers start: 27
  outliers final: 20
  residues processed: 146
  average time/residue: 0.0974
  time to fit residues: 20.1214
Evaluate side-chains
  150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1028 HIS
Chi-restraints excluded: chain A residue 1038 ASP
Chi-restraints excluded: chain A residue 1065 LYS
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1193 LEU
Chi-restraints excluded: chain A residue 1213 THR
Chi-restraints excluded: chain A residue 1223 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 42 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0050
   chunk 7 optimal weight:    1.9990
   chunk 91 optimal weight:   20.0000
   chunk 86 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 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 = 0.3882 r_free = 0.3882 target = 0.109914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.074688 restraints weight = 21628.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.89
r_work: 0.3100 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9240  Z= 0.128
  Angle     :  0.627  12.665  12529  Z= 0.309
  Chirality :  0.042   0.328   1449
  Planarity :  0.004   0.053   1575
  Dihedral  :  7.582 122.373   1403
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.44 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.25), residues: 1161
  helix:  2.31 (0.18), residues: 776
  sheet: -0.80 (0.97), residues: 31
  loop : -1.35 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1050 
 TYR   0.018   0.001   TYR A1122 
 PHE   0.012   0.001   PHE A 853 
 TRP   0.011   0.001   TRP A 950 
 HIS   0.003   0.001   HIS A 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9240)
  covalent geometry    : angle       0.62651 (12529)
  hydrogen bonds       : bond        0.04940 (  639)
  hydrogen bonds       : angle       4.37510 ( 1884)

********************** 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
  145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 GLN cc_start: 0.8591 (mm110) cc_final: 0.8389 (mm110)
REVERT: A  229 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8187 (mp)
REVERT: A  241 MET cc_start: 0.9131 (mtm) cc_final: 0.8783 (mtp)
REVERT: A  389 PHE cc_start: 0.9213 (t80) cc_final: 0.8962 (t80)
REVERT: A  488 PHE cc_start: 0.8454 (t80) cc_final: 0.8247 (t80)
REVERT: A  531 ASP cc_start: 0.7321 (t0) cc_final: 0.7037 (t70)
REVERT: A  796 GLU cc_start: 0.8035 (tp30) cc_final: 0.7719 (tp30)
REVERT: A  994 ARG cc_start: 0.8599 (ppt170) cc_final: 0.8310 (tmm-80)
REVERT: A 1117 TYR cc_start: 0.8572 (t80) cc_final: 0.8263 (t80)
REVERT: A 1118 GLU cc_start: 0.8800 (pt0) cc_final: 0.8575 (pp20)
REVERT: A 1129 GLU cc_start: 0.8724 (tp30) cc_final: 0.8425 (tp30)
  outliers start: 18
  outliers final: 17
  residues processed: 137
  average time/residue: 0.0946
  time to fit residues: 18.4736
Evaluate side-chains
  144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue 1028 HIS
Chi-restraints excluded: chain A residue 1038 ASP
Chi-restraints excluded: chain A residue 1065 LYS
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1193 LEU
Chi-restraints excluded: chain A residue 1213 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 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 = 0.3849 r_free = 0.3849 target = 0.107778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.072199 restraints weight = 21620.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.92
r_work: 0.3033 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9240  Z= 0.167
  Angle     :  0.644  12.735  12529  Z= 0.322
  Chirality :  0.043   0.335   1449
  Planarity :  0.004   0.058   1575
  Dihedral  :  7.641 121.095   1403
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 20.34 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.25), residues: 1161
  helix:  2.25 (0.18), residues: 776
  sheet: -1.14 (0.95), residues: 32
  loop : -1.31 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1043 
 TYR   0.019   0.002   TYR A1122 
 PHE   0.014   0.001   PHE A  72 
 TRP   0.009   0.001   TRP A 950 
 HIS   0.005   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9240)
  covalent geometry    : angle       0.64421 (12529)
  hydrogen bonds       : bond        0.05335 (  639)
  hydrogen bonds       : angle       4.45412 ( 1884)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2526.33 seconds
wall clock time: 44 minutes 4.31 seconds (2644.31 seconds total)