Starting phenix.real_space_refine
on Wed Apr 30 02:07:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jum_61830/04_2025/9jum_61830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jum_61830/04_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_61830/04_2025/9jum_61830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jum_61830/04_2025/9jum_61830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jum_61830/04_2025/9jum_61830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jum_61830/04_2025/9jum_61830.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.34, per 1000 atoms: 0.59
  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: 2.75
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      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: 0.95
  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: 3.18

  Time building geometry restraints manager: 3.15 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:             0.740
  Set stop_for_unknowns flag:              0.010
  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:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.430
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.500
-------------------------------------------------------------------------------
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 : 15.77
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.25), residues: 1161
  helix:  1.53 (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
 TRP   0.011   0.001   TRP A 441 
 HIS   0.006   0.001   HIS A  54 
 PHE   0.019   0.001   PHE A1144 
 TYR   0.021   0.002   TYR A 286 
 ARG   0.010   0.001   ARG A1050 

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

*********************** 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  : 0.938 
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: 0.2349
  time to fit residues: 50.6588
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  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 87 optimal weight:    0.8980
   chunk 48 optimal weight:   20.0000
   chunk 30 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9980
   chunk 105 optimal weight:   10.0000
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3861 r_free = 0.3861 target = 0.110205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.074306 restraints weight = 21551.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 3.02
r_work: 0.3040 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9240  Z= 0.146
  Angle     :  0.608   8.033  12529  Z= 0.315
  Chirality :  0.041   0.162   1449
  Planarity :  0.004   0.053   1575
  Dihedral  : 10.271 152.422   1403
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  8.64 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.25), residues: 1161
  helix:  2.04 (0.18), residues: 783
  sheet: -1.73 (1.01), residues: 31
  loop : -1.49 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 950 
 HIS   0.005   0.001   HIS A  54 
 PHE   0.015   0.001   PHE A  72 
 TYR   0.023   0.001   TYR A1122 
 ARG   0.005   0.001   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05712 (  639)
  hydrogen bonds       : angle       4.59614 ( 1884)
  covalent geometry    : bond        0.00293 ( 9240)
  covalent geometry    : angle       0.60830 (12529)

*********************** 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
  153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8194 (mp)
REVERT: A  241 MET cc_start: 0.9010 (mtp) cc_final: 0.8526 (mtp)
REVERT: A  421 ASP cc_start: 0.8750 (t70) cc_final: 0.8504 (t0)
REVERT: A  488 PHE cc_start: 0.8451 (t80) cc_final: 0.8166 (t80)
REVERT: A  507 LEU cc_start: 0.8357 (mm) cc_final: 0.8095 (mm)
REVERT: A  531 ASP cc_start: 0.7312 (t0) cc_final: 0.6963 (t70)
REVERT: A  796 GLU cc_start: 0.8279 (tp30) cc_final: 0.7982 (tp30)
REVERT: A  994 ARG cc_start: 0.8744 (ppt170) cc_final: 0.8477 (tmm-80)
REVERT: A 1007 GLU cc_start: 0.8576 (mp0) cc_final: 0.8340 (mp0)
REVERT: A 1048 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8271 (mmm-85)
REVERT: A 1075 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8303 (m-80)
REVERT: A 1117 TYR cc_start: 0.8557 (t80) cc_final: 0.8357 (t80)
REVERT: A 1129 GLU cc_start: 0.8851 (tp30) cc_final: 0.8637 (tp30)
REVERT: A 1134 GLN cc_start: 0.9070 (mp10) cc_final: 0.8724 (mp10)
REVERT: A 1169 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8788 (tm-30)
  outliers start: 12
  outliers final: 8
  residues processed: 143
  average time/residue: 0.2193
  time to fit residues: 44.2026
Evaluate side-chains
  135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
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  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 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 13 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 110 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 56 optimal weight:   20.0000
   chunk 23 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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
** 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 = 0.3852 r_free = 0.3852 target = 0.109537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.072555 restraints weight = 21883.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 3.05
r_work: 0.3015 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1565

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= 0.155
  Angle     :  0.591   7.116  12529  Z= 0.306
  Chirality :  0.041   0.157   1449
  Planarity :  0.004   0.056   1575
  Dihedral  :  9.002 155.713   1403
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.22 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.25), residues: 1161
  helix:  2.10 (0.18), residues: 782
  sheet: -0.62 (1.20), residues: 24
  loop : -1.47 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 950 
 HIS   0.006   0.001   HIS A  54 
 PHE   0.016   0.001   PHE A  72 
 TYR   0.030   0.001   TYR A1122 
 ARG   0.007   0.001   ARG A1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05526 (  639)
  hydrogen bonds       : angle       4.47369 ( 1884)
  covalent geometry    : bond        0.00328 ( 9240)
  covalent geometry    : angle       0.59073 (12529)

*********************** 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: 18
    poor density    : 134
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8189 (mp)
REVERT: A  241 MET cc_start: 0.8987 (mtp) cc_final: 0.8483 (mtp)
REVERT: A  421 ASP cc_start: 0.8754 (t70) cc_final: 0.8512 (t0)
REVERT: A  488 PHE cc_start: 0.8499 (t80) cc_final: 0.8233 (t80)
REVERT: A  507 LEU cc_start: 0.8398 (mm) cc_final: 0.8045 (mm)
REVERT: A  517 ILE cc_start: 0.9415 (mm) cc_final: 0.8984 (mm)
REVERT: A  521 MET cc_start: 0.8845 (mpp) cc_final: 0.8387 (mpp)
REVERT: A  531 ASP cc_start: 0.7251 (t0) cc_final: 0.6922 (t70)
REVERT: A  796 GLU cc_start: 0.8225 (tp30) cc_final: 0.7959 (tp30)
REVERT: A  994 ARG cc_start: 0.8748 (ppt170) cc_final: 0.8468 (tmm-80)
REVERT: A 1006 ILE cc_start: 0.9439 (mt) cc_final: 0.9222 (tp)
REVERT: A 1048 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.8451 (mmm-85)
REVERT: A 1050 ARG cc_start: 0.8487 (mmm160) cc_final: 0.8236 (mmm160)
REVERT: A 1075 PHE cc_start: 0.8846 (t80) cc_final: 0.8562 (m-80)
REVERT: A 1129 GLU cc_start: 0.8841 (tp30) cc_final: 0.8602 (tp30)
  outliers start: 18
  outliers final: 11
  residues processed: 140
  average time/residue: 0.2414
  time to fit residues: 48.0274
Evaluate side-chains
  139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
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  273 MET
Chi-restraints excluded: chain A residue  344 ILE
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 1104 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1259 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 112 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0170
   overall best weight:    2.0026

-------------------------------------------------------------------------------
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
** 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 = 0.3828 r_free = 0.3828 target = 0.107863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.072087 restraints weight = 21728.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.97
r_work: 0.2989 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9240  Z= 0.175
  Angle     :  0.604   9.083  12529  Z= 0.312
  Chirality :  0.041   0.196   1449
  Planarity :  0.004   0.058   1575
  Dihedral  :  8.421 151.938   1403
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.49 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.25), residues: 1161
  helix:  2.12 (0.18), residues: 782
  sheet: -0.63 (1.19), residues: 24
  loop : -1.49 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 950 
 HIS   0.007   0.001   HIS A  54 
 PHE   0.017   0.001   PHE A  72 
 TYR   0.026   0.002   TYR A1122 
 ARG   0.003   0.000   ARG A 519 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05608 (  639)
  hydrogen bonds       : angle       4.46135 ( 1884)
  covalent geometry    : bond        0.00383 ( 9240)
  covalent geometry    : angle       0.60404 (12529)

*********************** 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
  147 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8180 (mp)
REVERT: A  421 ASP cc_start: 0.8760 (t70) cc_final: 0.8540 (t0)
REVERT: A  488 PHE cc_start: 0.8463 (t80) cc_final: 0.8204 (t80)
REVERT: A  521 MET cc_start: 0.8695 (mpp) cc_final: 0.8366 (mtt)
REVERT: A  531 ASP cc_start: 0.7181 (t0) cc_final: 0.6844 (t70)
REVERT: A  796 GLU cc_start: 0.8183 (tp30) cc_final: 0.7882 (tp30)
REVERT: A  994 ARG cc_start: 0.8753 (ppt170) cc_final: 0.8488 (tmm-80)
  outliers start: 19
  outliers final: 13
  residues processed: 136
  average time/residue: 0.2071
  time to fit residues: 39.8387
Evaluate side-chains
  138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
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  273 MET
Chi-restraints excluded: chain A residue  344 ILE
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 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
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 75 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   chunk 101 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 95 optimal weight:    6.9990
   chunk 112 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 108 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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**
A 827 ASN
** 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 = 0.3818 r_free = 0.3818 target = 0.107327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.070627 restraints weight = 21779.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 3.01
r_work: 0.2967 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9240  Z= 0.191
  Angle     :  0.612   8.157  12529  Z= 0.319
  Chirality :  0.041   0.179   1449
  Planarity :  0.004   0.060   1575
  Dihedral  :  8.228 146.057   1403
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.60 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.25), residues: 1161
  helix:  2.03 (0.18), residues: 778
  sheet: -0.78 (1.16), residues: 24
  loop : -1.46 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 950 
 HIS   0.007   0.001   HIS A  54 
 PHE   0.017   0.002   PHE A  72 
 TYR   0.020   0.002   TYR A 286 
 ARG   0.005   0.000   ARG A1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05735 (  639)
  hydrogen bonds       : angle       4.51654 ( 1884)
  covalent geometry    : bond        0.00420 ( 9240)
  covalent geometry    : angle       0.61203 (12529)

*********************** 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
  151 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8206 (mp)
REVERT: A  241 MET cc_start: 0.9237 (mtm) cc_final: 0.8983 (mtp)
REVERT: A  488 PHE cc_start: 0.8479 (t80) cc_final: 0.8235 (t80)
REVERT: A  531 ASP cc_start: 0.7248 (t0) cc_final: 0.6911 (t70)
REVERT: A  796 GLU cc_start: 0.8181 (tp30) cc_final: 0.7859 (tp30)
REVERT: A  970 MET cc_start: 0.9243 (mmp) cc_final: 0.9039 (mmp)
REVERT: A  994 ARG cc_start: 0.8752 (ppt170) cc_final: 0.8472 (tmm-80)
  outliers start: 17
  outliers final: 14
  residues processed: 139
  average time/residue: 0.2290
  time to fit residues: 45.7031
Evaluate side-chains
  144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
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  273 MET
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 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
Chi-restraints excluded: chain A residue 1259 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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**
A 827 ASN
** 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 = 0.3816 r_free = 0.3816 target = 0.107247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.070471 restraints weight = 21624.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 3.03
r_work: 0.2966 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2127

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= 0.183
  Angle     :  0.615   9.479  12529  Z= 0.319
  Chirality :  0.041   0.192   1449
  Planarity :  0.004   0.058   1575
  Dihedral  :  8.066 138.832   1403
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.34 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.25), residues: 1161
  helix:  2.11 (0.18), residues: 772
  sheet: -0.92 (0.96), residues: 32
  loop : -1.38 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 950 
 HIS   0.006   0.001   HIS A  54 
 PHE   0.024   0.002   PHE A1112 
 TYR   0.018   0.001   TYR A 286 
 ARG   0.003   0.000   ARG A 519 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05704 (  639)
  hydrogen bonds       : angle       4.52310 ( 1884)
  covalent geometry    : bond        0.00403 ( 9240)
  covalent geometry    : angle       0.61518 (12529)

*********************** 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: 24
    poor density    : 132
  time to evaluate  : 0.980 
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  229 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8208 (mp)
REVERT: A  241 MET cc_start: 0.9280 (mtm) cc_final: 0.8888 (mtp)
REVERT: A  389 PHE cc_start: 0.9132 (t80) cc_final: 0.8910 (t80)
REVERT: A  488 PHE cc_start: 0.8461 (t80) cc_final: 0.8223 (t80)
REVERT: A  531 ASP cc_start: 0.7361 (t0) cc_final: 0.7020 (t70)
REVERT: A  546 GLN cc_start: 0.8739 (mp10) cc_final: 0.8536 (mp10)
REVERT: A  796 GLU cc_start: 0.8215 (tp30) cc_final: 0.7848 (tp30)
REVERT: A  994 ARG cc_start: 0.8739 (ppt170) cc_final: 0.8459 (tmm-80)
REVERT: A 1050 ARG cc_start: 0.9079 (mmt90) cc_final: 0.8819 (mmm160)
  outliers start: 24
  outliers final: 16
  residues processed: 146
  average time/residue: 0.2115
  time to fit residues: 43.1961
Evaluate side-chains
  142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  273 MET
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  527 ILE
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 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 1206 ASP
Chi-restraints excluded: chain A residue 1213 THR
Chi-restraints excluded: chain A residue 1259 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 108 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   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 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 = 0.3820 r_free = 0.3820 target = 0.107595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.070723 restraints weight = 21929.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 3.07
r_work: 0.2973 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2253

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= 0.168
  Angle     :  0.625   8.596  12529  Z= 0.320
  Chirality :  0.041   0.167   1449
  Planarity :  0.004   0.057   1575
  Dihedral  :  7.966 134.179   1403
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.25), residues: 1161
  helix:  2.13 (0.18), residues: 775
  sheet: -0.99 (0.94), residues: 32
  loop : -1.40 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 950 
 HIS   0.005   0.001   HIS A  54 
 PHE   0.014   0.001   PHE A  72 
 TYR   0.014   0.001   TYR A 286 
 ARG   0.004   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05583 (  639)
  hydrogen bonds       : angle       4.51620 ( 1884)
  covalent geometry    : bond        0.00365 ( 9240)
  covalent geometry    : angle       0.62516 (12529)

*********************** 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
  156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.976 
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: 0.8682 (mm110) cc_final: 0.8468 (tm-30)
REVERT: A  229 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7922 (mp)
REVERT: A  241 MET cc_start: 0.9209 (mtm) cc_final: 0.8830 (mtp)
REVERT: A  389 PHE cc_start: 0.9156 (t80) cc_final: 0.8882 (t80)
REVERT: A  488 PHE cc_start: 0.8468 (t80) cc_final: 0.8238 (t80)
REVERT: A  531 ASP cc_start: 0.7382 (t0) cc_final: 0.7035 (t70)
REVERT: A  546 GLN cc_start: 0.8711 (mp10) cc_final: 0.8498 (mp10)
REVERT: A  796 GLU cc_start: 0.8233 (tp30) cc_final: 0.7862 (tp30)
REVERT: A  970 MET cc_start: 0.9247 (mmp) cc_final: 0.8991 (mmp)
REVERT: A  994 ARG cc_start: 0.8713 (ppt170) cc_final: 0.8449 (tmm-80)
REVERT: A 1050 ARG cc_start: 0.9078 (mmt90) cc_final: 0.8705 (mmm160)
  outliers start: 24
  outliers final: 17
  residues processed: 146
  average time/residue: 0.2061
  time to fit residues: 42.7153
Evaluate side-chains
  147 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
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  273 MET
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  868 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 1206 ASP
Chi-restraints excluded: chain A residue 1213 THR
Chi-restraints excluded: chain A residue 1223 THR
Chi-restraints excluded: chain A residue 1259 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.3986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.108390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071703 restraints weight = 22011.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 3.08
r_work: 0.2991 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9240  Z= 0.149
  Angle     :  0.612   8.383  12529  Z= 0.313
  Chirality :  0.041   0.185   1449
  Planarity :  0.004   0.055   1575
  Dihedral  :  7.829 128.920   1403
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.25), residues: 1161
  helix:  2.14 (0.18), residues: 776
  sheet: -0.90 (0.97), residues: 32
  loop : -1.39 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 950 
 HIS   0.004   0.001   HIS A  54 
 PHE   0.021   0.001   PHE A1112 
 TYR   0.014   0.001   TYR A1122 
 ARG   0.004   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05374 (  639)
  hydrogen bonds       : angle       4.47112 ( 1884)
  covalent geometry    : bond        0.00321 ( 9240)
  covalent geometry    : angle       0.61238 (12529)

*********************** 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: 27
    poor density    : 134
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.7806 (mp)
REVERT: A  241 MET cc_start: 0.9168 (mtm) cc_final: 0.8789 (mtp)
REVERT: A  389 PHE cc_start: 0.9261 (t80) cc_final: 0.8932 (t80)
REVERT: A  488 PHE cc_start: 0.8472 (t80) cc_final: 0.8245 (t80)
REVERT: A  531 ASP cc_start: 0.7382 (t0) cc_final: 0.6978 (t70)
REVERT: A  546 GLN cc_start: 0.8725 (mp10) cc_final: 0.8413 (mp10)
REVERT: A  796 GLU cc_start: 0.8224 (tp30) cc_final: 0.7846 (tp30)
REVERT: A  970 MET cc_start: 0.9224 (mmp) cc_final: 0.8970 (mmp)
REVERT: A  994 ARG cc_start: 0.8672 (ppt170) cc_final: 0.8411 (tmm-80)
REVERT: A 1043 ARG cc_start: 0.8154 (mmt180) cc_final: 0.7899 (mmp80)
REVERT: A 1050 ARG cc_start: 0.9098 (mmt90) cc_final: 0.8734 (mmm160)
  outliers start: 27
  outliers final: 20
  residues processed: 148
  average time/residue: 0.2546
  time to fit residues: 53.4728
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  : 1.482 
-------------------------------------------------------------------------------
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  273 MET
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  806 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 1112 PHE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1193 LEU
Chi-restraints excluded: chain A residue 1206 ASP
Chi-restraints excluded: chain A residue 1213 THR
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 46 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1207 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.109121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.074061 restraints weight = 21680.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.90
r_work: 0.3085 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2578

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= 0.134
  Angle     :  0.624  12.353  12529  Z= 0.313
  Chirality :  0.041   0.239   1449
  Planarity :  0.004   0.053   1575
  Dihedral  :  7.702 125.476   1403
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.49 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.25), residues: 1161
  helix:  2.24 (0.18), residues: 773
  sheet: -0.76 (0.97), residues: 31
  loop : -1.35 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 950 
 HIS   0.003   0.001   HIS A  54 
 PHE   0.028   0.001   PHE A1112 
 TYR   0.010   0.001   TYR A1093 
 ARG   0.003   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05131 (  639)
  hydrogen bonds       : angle       4.42749 ( 1884)
  covalent geometry    : bond        0.00274 ( 9240)
  covalent geometry    : angle       0.62431 (12529)

*********************** 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
  165 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 1.284 
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  241 MET cc_start: 0.9084 (mtm) cc_final: 0.8783 (mtp)
REVERT: A  389 PHE cc_start: 0.9174 (t80) cc_final: 0.8891 (t80)
REVERT: A  488 PHE cc_start: 0.8489 (t80) cc_final: 0.8268 (t80)
REVERT: A  531 ASP cc_start: 0.7310 (t0) cc_final: 0.7033 (t70)
REVERT: A  546 GLN cc_start: 0.8748 (mp10) cc_final: 0.8355 (mp10)
REVERT: A  796 GLU cc_start: 0.8036 (tp30) cc_final: 0.7723 (tp30)
REVERT: A  994 ARG cc_start: 0.8594 (ppt170) cc_final: 0.8325 (tmm-80)
REVERT: A 1043 ARG cc_start: 0.8152 (mmt180) cc_final: 0.7900 (mmp80)
  outliers start: 24
  outliers final: 20
  residues processed: 153
  average time/residue: 0.2905
  time to fit residues: 63.0213
Evaluate side-chains
  151 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
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  582 VAL
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  833 VAL
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 1088 LYS
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 1206 ASP
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 49 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 115 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0870
   chunk 12 optimal weight:    0.0670
   chunk 57 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.5696

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** A 578 GLN ** 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 = 0.3884 r_free = 0.3884 target = 0.109811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.075051 restraints weight = 21867.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.91
r_work: 0.3095 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   9240  Z= 0.132
  Angle     :  0.636  12.252  12529  Z= 0.318
  Chirality :  0.042   0.308   1449
  Planarity :  0.004   0.052   1575
  Dihedral  :  7.611 123.446   1403
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 21.18 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.25), residues: 1161
  helix:  2.25 (0.18), residues: 774
  sheet: -0.96 (0.97), residues: 32
  loop : -1.34 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 950 
 HIS   0.003   0.001   HIS A 208 
 PHE   0.018   0.001   PHE A1112 
 TYR   0.013   0.001   TYR A1093 
 ARG   0.003   0.000   ARG A1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04972 (  639)
  hydrogen bonds       : angle       4.42037 ( 1884)
  covalent geometry    : bond        0.00269 ( 9240)
  covalent geometry    : angle       0.63568 (12529)

********************** 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
  148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.9268 (mtm) cc_final: 0.9013 (mtp)
REVERT: A  389 PHE cc_start: 0.9131 (t80) cc_final: 0.8928 (t80)
REVERT: A  488 PHE cc_start: 0.8518 (t80) cc_final: 0.8295 (t80)
REVERT: A  531 ASP cc_start: 0.7331 (t0) cc_final: 0.7038 (t70)
REVERT: A  796 GLU cc_start: 0.8058 (tp30) cc_final: 0.7794 (tp30)
REVERT: A  994 ARG cc_start: 0.8617 (ppt170) cc_final: 0.8327 (tmm-80)
REVERT: A 1043 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7863 (mmp80)
  outliers start: 18
  outliers final: 16
  residues processed: 142
  average time/residue: 0.2139
  time to fit residues: 43.0491
Evaluate side-chains
  140 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  275 LEU
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 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 1206 ASP
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 83 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 42 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.109769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.074874 restraints weight = 21809.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.91
r_work: 0.3136 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   9240  Z= 0.138
  Angle     :  0.657  12.672  12529  Z= 0.328
  Chirality :  0.042   0.340   1449
  Planarity :  0.004   0.052   1575
  Dihedral  :  7.572 122.042   1403
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 21.29 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.25), residues: 1161
  helix:  2.26 (0.18), residues: 774
  sheet: -1.06 (0.96), residues: 32
  loop : -1.31 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 950 
 HIS   0.003   0.001   HIS A  54 
 PHE   0.016   0.001   PHE A1112 
 TYR   0.008   0.001   TYR A 286 
 ARG   0.006   0.000   ARG A1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05011 (  639)
  hydrogen bonds       : angle       4.43507 ( 1884)
  covalent geometry    : bond        0.00292 ( 9240)
  covalent geometry    : angle       0.65739 (12529)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5689.05 seconds
wall clock time: 101 minutes 33.36 seconds (6093.36 seconds total)