Starting phenix.real_space_refine
on Fri Aug 22 18:21:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v5d_42982/08_2025/8v5d_42982.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v5d_42982/08_2025/8v5d_42982.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v5d_42982/08_2025/8v5d_42982.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v5d_42982/08_2025/8v5d_42982.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v5d_42982/08_2025/8v5d_42982.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v5d_42982/08_2025/8v5d_42982.map"
  }
  resolution = 3.0
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    4263      2.51       5
     N    1173      2.21       5
     O    1215      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6694
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 851, 6694
          Classifications: {'peptide': 851}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 793}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 41
          Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 35
  Time building chain proxies: 1.87, per 1000 atoms: 0.28
  Number of scatterers: 6694
  At special positions: 0
  Unit cell: (79.968, 94.129, 99.127, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1215      8.00
     N    1173      7.00
     C    4263      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: 0.59
  Conformation dependent library (CDL) restraints added in 464.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1578

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      46.7% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 80 through 89
    Processing helix  chain 'A' and resid 96 through 110
    Processing helix  chain 'A' and resid 134 through 159
      Proline residue:  A 149  - end of helix
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 240 through 244
      removed outlier: 3.731A  pdb=" N   LEU A 244 " --> pdb=" O   PRO A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 277
      removed outlier: 3.553A  pdb=" N   HIS A 277 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 283
      removed outlier: 3.986A  pdb=" N   TYR A 282 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 283 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 303
    Processing helix  chain 'A' and resid 355 through 364
    Processing helix  chain 'A' and resid 381 through 388
      removed outlier: 3.583A  pdb=" N   ILE A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 418
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'A' and resid 420 through 430
      removed outlier: 4.454A  pdb=" N   LEU A 424 " --> pdb=" O   HIS A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 470
      removed outlier: 3.653A  pdb=" N   ALA A 446 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 576
      removed outlier: 3.510A  pdb=" N   LYS A 575 " --> pdb=" O   GLY A 571 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU A 576 " --> pdb=" O   TRP A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 776
      removed outlier: 3.569A  pdb=" N   GLU A 775 " --> pdb=" O   LEU A 771 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP A 776 " --> pdb=" O   PRO A 772 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 771 through 776'
    Processing helix  chain 'A' and resid 788 through 810
      removed outlier: 3.582A  pdb=" N   LEU A 792 " --> pdb=" O   GLY A 788 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   PHE A 800 " --> pdb=" O   LYS A 796 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   TRP A 801 " --> pdb=" O   MET A 797 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN A 803 " --> pdb=" O   SER A 799 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 804 " --> pdb=" O   PHE A 800 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   LYS A 806 " --> pdb=" O   ARG A 802 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   ARG A 807 " --> pdb=" O   ASN A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 828
      removed outlier: 3.527A  pdb=" N   ILE A 826 " --> pdb=" O   PRO A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 875
      removed outlier: 4.245A  pdb=" N   LYS A 875 " --> pdb=" O   SER A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 908
    Processing helix  chain 'A' and resid 915 through 923
    Processing helix  chain 'A' and resid 930 through 940
    Processing helix  chain 'A' and resid 942 through 956
    Processing helix  chain 'A' and resid 958 through 970
    Processing helix  chain 'A' and resid 974 through 989
      removed outlier: 3.679A  pdb=" N   GLU A 980 " --> pdb=" O   GLN A 976 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA A 988 " --> pdb=" O   GLN A 984 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR A 989 " --> pdb=" O   MET A 985 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1066
      removed outlier: 3.783A  pdb=" N   PHE A1058 " --> pdb=" O   GLU A1054 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1089
    Processing helix  chain 'A' and resid 1092 through 1123
      removed outlier: 3.504A  pdb=" N   VAL A1100 " --> pdb=" O   ARG A1096 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   VAL A1101 " --> pdb=" O   VAL A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1146 through 1169
      removed outlier: 3.670A  pdb=" N   LEU A1168 " --> pdb=" O   PHE A1164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1205 through 1211
    Processing helix  chain 'A' and resid 1219 through 1228
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187
      removed outlier: 3.651A  pdb=" N   TRP A 175 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   CYS A 224 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   ALA A 200 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 196
      removed outlier: 6.196A  pdb=" N   LEU A 195 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   GLN A 264 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LEU A 292 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL A 266 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 438
    Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 607
    Processing sheet with id=AA5, first strand: chain 'A' and resid 612 through 615
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1127 through 1133
      removed outlier: 7.664A  pdb=" N   GLY A1127 " --> pdb=" O   ARG A1142 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ARG A1142 " --> pdb=" O   GLY A1127 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   PHE A1129 " --> pdb=" O   LEU A1140 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   LEU A1140 " --> pdb=" O   PHE A1129 " (cutoff:3.500A)

    288 hydrogen bonds defined for protein.
    831 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: 1.14

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2216
        1.34 -     1.46: 1501
        1.46 -     1.58: 3083
        1.58 -     1.69: 0
        1.69 -     1.81: 71
  Bond restraints: 6871
  Sorted by residual:
  bond pdb=" CA  VAL A 878 "
       pdb=" CB  VAL A 878 "
    ideal  model  delta    sigma   weight residual
    1.540  1.525  0.015 1.36e-02 5.41e+03 1.21e+00
  bond pdb=" N   PRO A 246 "
       pdb=" CA  PRO A 246 "
    ideal  model  delta    sigma   weight residual
    1.469  1.482 -0.014 1.28e-02 6.10e+03 1.14e+00
  bond pdb=" CA  THR A 914 "
       pdb=" C   THR A 914 "
    ideal  model  delta    sigma   weight residual
    1.522  1.508  0.014 1.37e-02 5.33e+03 1.06e+00
  bond pdb=" CA  ALA A 604 "
       pdb=" C   ALA A 604 "
    ideal  model  delta    sigma   weight residual
    1.532  1.523  0.009 9.60e-03 1.09e+04 9.28e-01
  bond pdb=" N   PRO A 163 "
       pdb=" CA  PRO A 163 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.31e-02 5.83e+03 7.70e-01
  ... (remaining 6866 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 8878
        1.01 -     2.03: 346
        2.03 -     3.04: 87
        3.04 -     4.06: 18
        4.06 -     5.07: 10
  Bond angle restraints: 9339
  Sorted by residual:
  angle pdb=" CA  GLY A1205 "
        pdb=" C   GLY A1205 "
        pdb=" O   GLY A1205 "
      ideal   model   delta    sigma   weight residual
     122.37  120.22    2.15 7.30e-01 1.88e+00 8.67e+00
  angle pdb=" CA  GLY A1205 "
        pdb=" C   GLY A1205 "
        pdb=" N   MET A1206 "
      ideal   model   delta    sigma   weight residual
     114.13  116.99   -2.86 1.11e+00 8.12e-01 6.62e+00
  angle pdb=" O   THR A 914 "
        pdb=" C   THR A 914 "
        pdb=" N   ALA A 915 "
      ideal   model   delta    sigma   weight residual
     122.43  125.76   -3.33 1.46e+00 4.69e-01 5.20e+00
  angle pdb=" CA  THR A 914 "
        pdb=" C   THR A 914 "
        pdb=" N   ALA A 915 "
      ideal   model   delta    sigma   weight residual
     118.41  115.43    2.98 1.34e+00 5.57e-01 4.93e+00
  angle pdb=" C   ILE A 245 "
        pdb=" N   PRO A 246 "
        pdb=" CA  PRO A 246 "
      ideal   model   delta    sigma   weight residual
     119.84  122.59   -2.75 1.25e+00 6.40e-01 4.82e+00
  ... (remaining 9334 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 3875
       16.24 -    32.48: 182
       32.48 -    48.73: 35
       48.73 -    64.97: 3
       64.97 -    81.21: 2
  Dihedral angle restraints: 4097
    sinusoidal: 1648
      harmonic: 2449
  Sorted by residual:
  dihedral pdb=" CA  SER A 810 "
           pdb=" C   SER A 810 "
           pdb=" N   GLN A 811 "
           pdb=" CA  GLN A 811 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.61   16.39     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  ARG A 869 "
           pdb=" CB  ARG A 869 "
           pdb=" CG  ARG A 869 "
           pdb=" CD  ARG A 869 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.19  -57.81     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" N   PHE A1164 "
           pdb=" CA  PHE A1164 "
           pdb=" CB  PHE A1164 "
           pdb=" CG  PHE A1164 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -128.38  -51.62     3      1.50e+01 4.44e-03 9.03e+00
  ... (remaining 4094 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 602
       0.028 -    0.055: 258
       0.055 -    0.083: 79
       0.083 -    0.110: 53
       0.110 -    0.138: 12
  Chirality restraints: 1004
  Sorted by residual:
  chirality pdb=" CA  ILE A 245 "
            pdb=" N   ILE A 245 "
            pdb=" C   ILE A 245 "
            pdb=" CB  ILE A 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  VAL A 845 "
            pdb=" N   VAL A 845 "
            pdb=" C   VAL A 845 "
            pdb=" CB  VAL A 845 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.69e-01
  chirality pdb=" CA  ILE A1185 "
            pdb=" N   ILE A1185 "
            pdb=" C   ILE A1185 "
            pdb=" CB  ILE A1185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 1001 not shown)

  Planarity restraints: 1214
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  72 "    0.033 5.00e-02 4.00e+02   5.01e-02 4.02e+00
        pdb=" N   PRO A  73 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A  73 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  73 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 588 "   -0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO A 589 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 589 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 589 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 240 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.14e+00
        pdb=" N   PRO A 241 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 241 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 241 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1211 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 990
        2.75 -     3.29: 6349
        3.29 -     3.83: 11352
        3.83 -     4.36: 12933
        4.36 -     4.90: 22597
  Nonbonded interactions: 54221
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 990 "
            pdb=" OG  SER A1055 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   MET A 797 "
            pdb=" N   VAL A 870 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" NH2 ARG A 417 "
            pdb=" O   ILE A1079 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" O   ASN A 795 "
            pdb=" OG  SER A 799 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   ALA A 957 "
            pdb=" OH  TYR A 986 "
     model   vdw
     2.246 3.040
  ... (remaining 54216 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:             3.030
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.710
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5967
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      :  0.003   0.035   6871  Z= 0.141
  Angle     :  0.519   5.071   9339  Z= 0.280
  Chirality :  0.039   0.138   1004
  Planarity :  0.004   0.050   1214
  Dihedral  :  9.897  81.209   2519
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  4.26 %
    Favored  : 93.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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:  0.80 (0.29), residues: 837
  helix:  1.52 (0.28), residues: 345
  sheet:  0.76 (0.61), residues: 82
  loop : -0.33 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 869 
 TYR   0.010   0.001   TYR A1166 
 PHE   0.010   0.001   PHE A 389 
 TRP   0.011   0.001   TRP A 859 
 HIS   0.005   0.001   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6871)
  covalent geometry    : angle       0.51884 ( 9339)
  hydrogen bonds       : bond        0.18521 (  288)
  hydrogen bonds       : angle       8.07056 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 TYR cc_start: 0.6369 (t80) cc_final: 0.5555 (t80)
REVERT: A  452 TYR cc_start: 0.7765 (t80) cc_final: 0.6909 (t80)
REVERT: A  907 PHE cc_start: 0.6614 (t80) cc_final: 0.6252 (t80)
REVERT: A  986 TYR cc_start: 0.7064 (m-80) cc_final: 0.6436 (m-80)
  outliers start: 13
  outliers final: 4
  residues processed: 178
  average time/residue: 0.5466
  time to fit residues: 102.4903
Evaluate side-chains
  107 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  929 THR
Chi-restraints excluded: chain A residue 1184 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0070
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
A 134 ASN
A 161 GLN
A 390 GLN
A 398 GLN
A 569 HIS
A 805 HIS
A 906 HIS
** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 GLN
A 968 GLN
A 971 HIS
A1157 ASN
A1214 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4999 r_free = 0.4999 target = 0.204544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.174039 restraints weight = 12119.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.4690 rms_B_bonded: 3.87
r_work: 0.4530 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.4530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6108
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6871  Z= 0.175
  Angle     :  0.694   9.834   9339  Z= 0.346
  Chirality :  0.044   0.181   1004
  Planarity :  0.005   0.053   1214
  Dihedral  :  4.361  34.158    928
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 14.75 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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:  0.50 (0.29), residues: 837
  helix:  1.10 (0.27), residues: 349
  sheet:  0.60 (0.56), residues: 89
  loop : -0.36 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 457 
 TYR   0.028   0.002   TYR A 452 
 PHE   0.019   0.002   PHE A 969 
 TRP   0.012   0.002   TRP A 918 
 HIS   0.007   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 6871)
  covalent geometry    : angle       0.69378 ( 9339)
  hydrogen bonds       : bond        0.04511 (  288)
  hydrogen bonds       : angle       6.24655 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 TYR cc_start: 0.6674 (t80) cc_final: 0.5928 (t80)
REVERT: A  831 TYR cc_start: 0.7422 (t80) cc_final: 0.7186 (t80)
REVERT: A  907 PHE cc_start: 0.7055 (t80) cc_final: 0.6584 (t80)
REVERT: A 1108 TYR cc_start: 0.7678 (t80) cc_final: 0.7475 (t80)
REVERT: A 1153 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5383 (mp)
  outliers start: 24
  outliers final: 7
  residues processed: 124
  average time/residue: 0.5173
  time to fit residues: 67.7792
Evaluate side-chains
  94 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  734 HIS
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1184 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 30 optimal weight:    0.3980
   chunk 72 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 35 optimal weight:    0.2980
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 971 HIS
A1175 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.201534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.170665 restraints weight = 11922.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.4578 rms_B_bonded: 4.06
r_work: 0.4421 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.4421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6101
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6871  Z= 0.216
  Angle     :  0.757  15.425   9339  Z= 0.370
  Chirality :  0.045   0.242   1004
  Planarity :  0.005   0.057   1214
  Dihedral  :  4.668  34.900    925
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 16.74 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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:  0.01 (0.29), residues: 837
  helix:  0.64 (0.27), residues: 356
  sheet:  0.06 (0.55), residues: 88
  loop : -0.52 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 802 
 TYR   0.015   0.002   TYR A1166 
 PHE   0.012   0.002   PHE A 800 
 TRP   0.022   0.002   TRP A 585 
 HIS   0.008   0.001   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 6871)
  covalent geometry    : angle       0.75693 ( 9339)
  hydrogen bonds       : bond        0.04579 (  288)
  hydrogen bonds       : angle       6.06269 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 TYR cc_start: 0.6895 (t80) cc_final: 0.5788 (t80)
REVERT: A  831 TYR cc_start: 0.7708 (t80) cc_final: 0.7506 (t80)
REVERT: A  877 MET cc_start: 0.8121 (tpp) cc_final: 0.7623 (mpp)
REVERT: A  907 PHE cc_start: 0.7048 (t80) cc_final: 0.6590 (t80)
REVERT: A 1058 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6028 (m-80)
REVERT: A 1062 GLU cc_start: 0.6031 (mm-30) cc_final: 0.4083 (pp20)
REVERT: A 1108 TYR cc_start: 0.8094 (t80) cc_final: 0.7693 (t80)
REVERT: A 1153 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5297 (mp)
REVERT: A 1163 MET cc_start: 0.5270 (tmm) cc_final: 0.4737 (tpt)
  outliers start: 28
  outliers final: 8
  residues processed: 110
  average time/residue: 0.3892
  time to fit residues: 45.5532
Evaluate side-chains
  91 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  734 HIS
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue 1058 PHE
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1184 ASP
Chi-restraints excluded: chain A residue 1220 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 70 optimal weight:    9.9990
   chunk 61 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0870
   chunk 77 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0770
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
A 144 GLN
A1171 ASN
A1175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4970 r_free = 0.4970 target = 0.204220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.173996 restraints weight = 11888.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.4651 rms_B_bonded: 4.00
r_work: 0.4498 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.4498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6008
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6871  Z= 0.136
  Angle     :  0.679  14.936   9339  Z= 0.326
  Chirality :  0.044   0.197   1004
  Planarity :  0.004   0.054   1214
  Dihedral  :  4.521  31.704    925
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.87 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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:  0.15 (0.29), residues: 837
  helix:  0.69 (0.27), residues: 363
  sheet: -0.07 (0.55), residues: 91
  loop : -0.32 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 802 
 TYR   0.013   0.001   TYR A 395 
 PHE   0.008   0.001   PHE A 273 
 TRP   0.012   0.001   TRP A 748 
 HIS   0.014   0.001   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6871)
  covalent geometry    : angle       0.67854 ( 9339)
  hydrogen bonds       : bond        0.03827 (  288)
  hydrogen bonds       : angle       5.66355 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7108 (tp30)
REVERT: A  444 TYR cc_start: 0.6681 (t80) cc_final: 0.6112 (t80)
REVERT: A  449 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6402 (pp30)
REVERT: A  774 MET cc_start: 0.5874 (OUTLIER) cc_final: 0.5415 (mpp)
REVERT: A  907 PHE cc_start: 0.7015 (t80) cc_final: 0.6627 (t80)
REVERT: A 1062 GLU cc_start: 0.5975 (mm-30) cc_final: 0.4146 (pp20)
REVERT: A 1108 TYR cc_start: 0.8012 (t80) cc_final: 0.7531 (t80)
REVERT: A 1153 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.5245 (mp)
REVERT: A 1163 MET cc_start: 0.5191 (tmm) cc_final: 0.4501 (tpt)
  outliers start: 22
  outliers final: 6
  residues processed: 112
  average time/residue: 0.4180
  time to fit residues: 49.8188
Evaluate side-chains
  92 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain A residue  734 HIS
Chi-restraints excluded: chain A residue  774 MET
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1184 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4930 r_free = 0.4930 target = 0.199586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.167837 restraints weight = 12173.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.4576 rms_B_bonded: 4.07
r_work: 0.4423 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.4423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6163
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6871  Z= 0.232
  Angle     :  0.775  12.979   9339  Z= 0.375
  Chirality :  0.046   0.149   1004
  Planarity :  0.005   0.064   1214
  Dihedral  :  4.816  28.512    925
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.71 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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: -0.24 (0.29), residues: 837
  helix:  0.32 (0.27), residues: 365
  sheet: -0.30 (0.57), residues: 86
  loop : -0.47 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1138 
 TYR   0.021   0.002   TYR A 831 
 PHE   0.035   0.002   PHE A 139 
 TRP   0.012   0.002   TRP A 801 
 HIS   0.013   0.002   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 6871)
  covalent geometry    : angle       0.77487 ( 9339)
  hydrogen bonds       : bond        0.04583 (  288)
  hydrogen bonds       : angle       5.82631 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7106 (tp30)
REVERT: A  430 MET cc_start: 0.5400 (OUTLIER) cc_final: 0.5103 (ttm)
REVERT: A  449 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6583 (pp30)
REVERT: A  877 MET cc_start: 0.8112 (tpp) cc_final: 0.7792 (mmp)
REVERT: A  907 PHE cc_start: 0.7098 (t80) cc_final: 0.6654 (t80)
REVERT: A 1062 GLU cc_start: 0.5942 (mm-30) cc_final: 0.4038 (pp20)
REVERT: A 1093 MET cc_start: 0.3172 (tpp) cc_final: 0.2823 (tpp)
REVERT: A 1108 TYR cc_start: 0.8074 (t80) cc_final: 0.7859 (t80)
REVERT: A 1153 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5564 (mt)
REVERT: A 1163 MET cc_start: 0.5404 (tmm) cc_final: 0.4807 (tpt)
  outliers start: 27
  outliers final: 10
  residues processed: 107
  average time/residue: 0.4321
  time to fit residues: 49.3360
Evaluate side-chains
  95 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain A residue  459 MET
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain A residue 1080 SER
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1184 ASP
Chi-restraints excluded: chain A residue 1220 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 80 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1175 GLN
** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4954 r_free = 0.4954 target = 0.199876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.168824 restraints weight = 12119.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.4616 rms_B_bonded: 3.89
r_work: 0.4469 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.4469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6225
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6871  Z= 0.174
  Angle     :  0.719  11.964   9339  Z= 0.346
  Chirality :  0.045   0.167   1004
  Planarity :  0.005   0.060   1214
  Dihedral  :  4.785  27.642    925
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.56 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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: -0.13 (0.29), residues: 837
  helix:  0.51 (0.27), residues: 363
  sheet:  0.02 (0.63), residues: 68
  loop : -0.57 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1138 
 TYR   0.014   0.002   TYR A 831 
 PHE   0.017   0.002   PHE A 139 
 TRP   0.014   0.002   TRP A 801 
 HIS   0.012   0.001   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6871)
  covalent geometry    : angle       0.71945 ( 9339)
  hydrogen bonds       : bond        0.04136 (  288)
  hydrogen bonds       : angle       5.72628 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7179 (tp30)
REVERT: A  430 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5429 (ttm)
REVERT: A  444 TYR cc_start: 0.6508 (t80) cc_final: 0.5828 (t80)
REVERT: A  449 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.6047 (pp30)
REVERT: A  774 MET cc_start: 0.5482 (mpp) cc_final: 0.4509 (mmm)
REVERT: A  798 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7503 (pp)
REVERT: A  877 MET cc_start: 0.7882 (tpp) cc_final: 0.7615 (mpp)
REVERT: A  907 PHE cc_start: 0.7135 (t80) cc_final: 0.6773 (t80)
REVERT: A  910 MET cc_start: 0.5909 (mtp) cc_final: 0.5655 (ttp)
REVERT: A  985 MET cc_start: 0.7640 (tmm) cc_final: 0.6750 (ppp)
REVERT: A  986 TYR cc_start: 0.6618 (OUTLIER) cc_final: 0.4211 (m-80)
REVERT: A 1062 GLU cc_start: 0.5928 (mm-30) cc_final: 0.3886 (pt0)
REVERT: A 1153 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5850 (mp)
REVERT: A 1163 MET cc_start: 0.5677 (tmm) cc_final: 0.5061 (tpt)
  outliers start: 26
  outliers final: 7
  residues processed: 102
  average time/residue: 0.4038
  time to fit residues: 44.0086
Evaluate side-chains
  93 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain A residue  734 HIS
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  986 TYR
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1184 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 64 optimal weight:    9.9990
   chunk 56 optimal weight:    0.0370
   chunk 68 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.1664

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

Flipped N/Q/H residues before XYZ refinement:
** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.198374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.167932 restraints weight = 12087.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.4600 rms_B_bonded: 3.88
r_work: 0.4449 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.4449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6241
moved from start:          0.4420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6871  Z= 0.179
  Angle     :  0.741  15.861   9339  Z= 0.353
  Chirality :  0.045   0.173   1004
  Planarity :  0.005   0.069   1214
  Dihedral  :  4.793  27.962    925
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.84 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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: -0.27 (0.29), residues: 837
  helix:  0.45 (0.27), residues: 362
  sheet: -0.32 (0.61), residues: 78
  loop : -0.65 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 288 
 TYR   0.028   0.002   TYR A1108 
 PHE   0.026   0.002   PHE A 139 
 TRP   0.023   0.002   TRP A 748 
 HIS   0.011   0.001   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 6871)
  covalent geometry    : angle       0.74084 ( 9339)
  hydrogen bonds       : bond        0.04268 (  288)
  hydrogen bonds       : angle       5.74697 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.6634 (tm) cc_final: 0.6164 (pt)
REVERT: A  429 GLU cc_start: 0.6334 (mp0) cc_final: 0.6117 (mp0)
REVERT: A  430 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5495 (ttm)
REVERT: A  449 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.6107 (pp30)
REVERT: A  774 MET cc_start: 0.5621 (mpp) cc_final: 0.4456 (mmm)
REVERT: A  798 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7477 (pp)
REVERT: A  907 PHE cc_start: 0.7087 (t80) cc_final: 0.6645 (t80)
REVERT: A  910 MET cc_start: 0.5855 (mtp) cc_final: 0.5545 (ttp)
REVERT: A  985 MET cc_start: 0.7758 (tmm) cc_final: 0.6707 (pp-130)
REVERT: A  986 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.4046 (m-80)
REVERT: A 1062 GLU cc_start: 0.5912 (mm-30) cc_final: 0.3743 (pt0)
REVERT: A 1153 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5954 (mp)
REVERT: A 1163 MET cc_start: 0.5761 (tmm) cc_final: 0.5135 (tpt)
  outliers start: 21
  outliers final: 9
  residues processed: 96
  average time/residue: 0.4335
  time to fit residues: 44.5374
Evaluate side-chains
  93 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  734 HIS
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  986 TYR
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1184 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 55 optimal weight:    0.3980
   chunk 12 optimal weight:    0.2980
   chunk 45 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    0.1980
   chunk 77 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 795 ASN
** A 932 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 = 0.4962 r_free = 0.4962 target = 0.201391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.171365 restraints weight = 11887.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.4639 rms_B_bonded: 3.77
r_work: 0.4494 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.4494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6155
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6871  Z= 0.142
  Angle     :  0.739  18.391   9339  Z= 0.347
  Chirality :  0.045   0.172   1004
  Planarity :  0.005   0.061   1214
  Dihedral  :  4.659  25.912    925
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.66 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.83 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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: -0.13 (0.29), residues: 837
  helix:  0.56 (0.27), residues: 362
  sheet: -0.47 (0.59), residues: 81
  loop : -0.51 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 227 
 TYR   0.025   0.002   TYR A 444 
 PHE   0.012   0.001   PHE A 139 
 TRP   0.022   0.001   TRP A 748 
 HIS   0.011   0.001   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6871)
  covalent geometry    : angle       0.73907 ( 9339)
  hydrogen bonds       : bond        0.03962 (  288)
  hydrogen bonds       : angle       5.68511 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.6312 (tm) cc_final: 0.6042 (pt)
REVERT: A  375 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7171 (tp30)
REVERT: A  429 GLU cc_start: 0.6244 (mp0) cc_final: 0.6036 (mp0)
REVERT: A  430 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.5500 (ttm)
REVERT: A  449 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.5947 (pp30)
REVERT: A  603 MET cc_start: 0.7266 (pmm) cc_final: 0.6948 (ppp)
REVERT: A  774 MET cc_start: 0.5489 (mpp) cc_final: 0.4447 (mmm)
REVERT: A  798 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7395 (pp)
REVERT: A  907 PHE cc_start: 0.7030 (t80) cc_final: 0.6661 (t80)
REVERT: A  910 MET cc_start: 0.5887 (mtp) cc_final: 0.5570 (ttp)
REVERT: A  985 MET cc_start: 0.7706 (tmm) cc_final: 0.6657 (pp-130)
REVERT: A  986 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.3988 (m-80)
REVERT: A 1062 GLU cc_start: 0.5871 (mm-30) cc_final: 0.3743 (pt0)
REVERT: A 1153 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5741 (mp)
REVERT: A 1163 MET cc_start: 0.5647 (tmm) cc_final: 0.5044 (tpt)
  outliers start: 23
  outliers final: 8
  residues processed: 105
  average time/residue: 0.4094
  time to fit residues: 45.9606
Evaluate side-chains
  94 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  597 ARG
Chi-restraints excluded: chain A residue  734 HIS
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  986 TYR
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1184 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 63 optimal weight:    0.1980
   overall best weight:    2.0388

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
** A 932 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 = 0.4909 r_free = 0.4909 target = 0.195538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.164171 restraints weight = 12291.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.4553 rms_B_bonded: 3.91
r_work: 0.4403 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6349
moved from start:          0.4867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082   6871  Z= 0.265
  Angle     :  0.889  17.522   9339  Z= 0.423
  Chirality :  0.049   0.215   1004
  Planarity :  0.006   0.069   1214
  Dihedral  :  5.099  29.558    925
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 19.95
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.33 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 24.40 %
    Favored  : 72.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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: -0.60 (0.29), residues: 837
  helix:  0.22 (0.27), residues: 347
  sheet: -0.61 (0.59), residues: 78
  loop : -0.82 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 288 
 TYR   0.027   0.002   TYR A 444 
 PHE   0.028   0.002   PHE A 139 
 TRP   0.020   0.002   TRP A 748 
 HIS   0.011   0.002   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 ( 6871)
  covalent geometry    : angle       0.88911 ( 9339)
  hydrogen bonds       : bond        0.05044 (  288)
  hydrogen bonds       : angle       6.07147 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.6593 (tm) cc_final: 0.6244 (pt)
REVERT: A  429 GLU cc_start: 0.6253 (mp0) cc_final: 0.6046 (mp0)
REVERT: A  430 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.5323 (ttm)
REVERT: A  449 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.6241 (pp30)
REVERT: A  597 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7630 (tpt170)
REVERT: A  603 MET cc_start: 0.7349 (pmm) cc_final: 0.7042 (ppp)
REVERT: A  774 MET cc_start: 0.5580 (mpp) cc_final: 0.4427 (mmm)
REVERT: A  798 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7433 (pp)
REVERT: A  907 PHE cc_start: 0.7157 (t80) cc_final: 0.6727 (t80)
REVERT: A  910 MET cc_start: 0.6266 (mtp) cc_final: 0.5597 (mtm)
REVERT: A  985 MET cc_start: 0.7798 (tmm) cc_final: 0.6947 (ppp)
REVERT: A  986 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.4029 (m-80)
REVERT: A 1062 GLU cc_start: 0.5777 (mm-30) cc_final: 0.3488 (pt0)
REVERT: A 1153 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5876 (mt)
  outliers start: 25
  outliers final: 8
  residues processed: 102
  average time/residue: 0.4214
  time to fit residues: 46.0277
Evaluate side-chains
  91 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  597 ARG
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  986 TYR
Chi-restraints excluded: chain A residue 1080 SER
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1155 ILE
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1184 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0670
   chunk 75 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0020
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.4726

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 932 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 = 0.4958 r_free = 0.4958 target = 0.200814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.170804 restraints weight = 12185.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.4625 rms_B_bonded: 3.92
r_work: 0.4477 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.4477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6155
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6871  Z= 0.151
  Angle     :  0.809  19.636   9339  Z= 0.374
  Chirality :  0.046   0.182   1004
  Planarity :  0.005   0.062   1214
  Dihedral  :  4.799  25.840    924
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.66 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 26.10 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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: -0.38 (0.29), residues: 837
  helix:  0.40 (0.27), residues: 363
  sheet: -0.66 (0.59), residues: 81
  loop : -0.70 (0.33), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 227 
 TYR   0.024   0.002   TYR A 444 
 PHE   0.010   0.001   PHE A 139 
 TRP   0.018   0.002   TRP A 748 
 HIS   0.011   0.001   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6871)
  covalent geometry    : angle       0.80899 ( 9339)
  hydrogen bonds       : bond        0.04056 (  288)
  hydrogen bonds       : angle       5.83258 (  831)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  603 MET cc_start: 0.7318 (pmm) cc_final: 0.6954 (ppp)
REVERT: A  774 MET cc_start: 0.5643 (mpp) cc_final: 0.4730 (mmm)
REVERT: A  798 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7450 (pp)
REVERT: A  907 PHE cc_start: 0.7042 (t80) cc_final: 0.6620 (t80)
REVERT: A  910 MET cc_start: 0.6003 (mtp) cc_final: 0.5659 (ttp)
REVERT: A  985 MET cc_start: 0.7751 (tmm) cc_final: 0.6788 (pp-130)
REVERT: A  986 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.3988 (m-80)
REVERT: A 1062 GLU cc_start: 0.5833 (mm-30) cc_final: 0.3761 (pt0)
REVERT: A 1153 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5657 (mp)
  outliers start: 14
  outliers final: 7
  residues processed: 93
  average time/residue: 0.4506
  time to fit residues: 44.4448
Evaluate side-chains
  86 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  986 TYR
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1155 ILE
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1184 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 40 optimal weight:   20.0000
   chunk 84 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 932 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 = 0.4955 r_free = 0.4955 target = 0.199993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.169285 restraints weight = 12168.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.4615 rms_B_bonded: 3.86
r_work: 0.4462 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.4462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6216
moved from start:          0.5027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   6871  Z= 0.169
  Angle     :  0.824  18.391   9339  Z= 0.385
  Chirality :  0.046   0.179   1004
  Planarity :  0.005   0.062   1214
  Dihedral  :  4.775  26.311    924
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.50 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 26.10 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    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: -0.47 (0.29), residues: 837
  helix:  0.24 (0.27), residues: 368
  sheet: -0.46 (0.60), residues: 78
  loop : -0.71 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 227 
 TYR   0.028   0.002   TYR A 444 
 PHE   0.015   0.001   PHE A 139 
 TRP   0.023   0.002   TRP A 748 
 HIS   0.011   0.001   HIS A 971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6871)
  covalent geometry    : angle       0.82417 ( 9339)
  hydrogen bonds       : bond        0.04223 (  288)
  hydrogen bonds       : angle       5.85837 (  831)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2256.94 seconds
wall clock time: 39 minutes 16.47 seconds (2356.47 seconds total)