Starting phenix.real_space_refine
on Tue Mar  3 15:52:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pd4_13330/03_2026/7pd4_13330.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pd4_13330/03_2026/7pd4_13330.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pd4_13330/03_2026/7pd4_13330.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pd4_13330/03_2026/7pd4_13330.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pd4_13330/03_2026/7pd4_13330.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pd4_13330/03_2026/7pd4_13330.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      55      5.16       5
     C    4329      2.51       5
     N    1098      2.21       5
     O    1194      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6676
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 842, 6676
          Classifications: {'peptide': 842}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 20, 'TRANS': 821}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 1.64, per 1000 atoms: 0.25
  Number of scatterers: 6676
  At special positions: 0
  Unit cell: (82.62, 78.57, 144.99, 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      55     16.00
     O    1194      8.00
     N    1098      7.00
     C    4329      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: 0.68
  Conformation dependent library (CDL) restraints added in 246.9 milliseconds
  

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 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 4 sheets defined
      65.4% alpha, 18.6% 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 97 through 108
      removed outlier: 3.539A  pdb=" N   MET A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 137
      removed outlier: 4.130A  pdb=" N   THR A 112 " --> pdb=" O   CYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 164
      removed outlier: 4.377A  pdb=" N   PHE A 164 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 169
      removed outlier: 3.891A  pdb=" N   ALA A 169 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 192
    Processing helix  chain 'A' and resid 219 through 237
      removed outlier: 4.399A  pdb=" N   SER A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 260
    Processing helix  chain 'A' and resid 279 through 336
    Processing helix  chain 'A' and resid 339 through 348
      removed outlier: 3.704A  pdb=" N   LYS A 348 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 359
      removed outlier: 4.297A  pdb=" N   GLU A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 413 through 434
    Processing helix  chain 'A' and resid 457 through 478
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 3.621A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 540
      removed outlier: 4.207A  pdb=" N   TYR A 538 " --> pdb=" O   ALA A 534 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ASP A 540 " --> pdb=" O   ALA A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 807
    Processing helix  chain 'A' and resid 817 through 844
      removed outlier: 4.476A  pdb=" N   LEU A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 858
      removed outlier: 4.325A  pdb=" N   LYS A 853 " --> pdb=" O   MET A 849 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TRP A 858 " --> pdb=" O   ARG A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 875
    Processing helix  chain 'A' and resid 875 through 885
      removed outlier: 4.035A  pdb=" N   HIS A 883 " --> pdb=" O   ALA A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 907
    Processing helix  chain 'A' and resid 908 through 911
    Processing helix  chain 'A' and resid 917 through 938
      Proline residue:  A 931  - end of helix
    Processing helix  chain 'A' and resid 978 through 1037
    Processing helix  chain 'A' and resid 1039 through 1048
    Processing helix  chain 'A' and resid 1067 through 1072
      removed outlier: 3.677A  pdb=" N   PHE A1071 " --> pdb=" O   ASN A1067 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1098
    Processing helix  chain 'A' and resid 1134 through 1157
      removed outlier: 3.512A  pdb=" N   ASN A1155 " --> pdb=" O   ASP A1151 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASN A1156 " --> pdb=" O   ASP A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1189 through 1201
      removed outlier: 3.946A  pdb=" N   ASN A1193 " --> pdb=" O   GLY A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1211 through 1219
    Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 441
      removed outlier: 5.473A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 441
      removed outlier: 5.473A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 8.584A  pdb=" N   HIS A 530 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   VAL A 488 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1105 through 1107
      removed outlier: 3.763A  pdb=" N   SER A1119 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   GLY A1171 " --> pdb=" O   SER A1057 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   GLY A1059 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ASN A1169 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   ILE A1061 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLY A1167 " --> pdb=" O   ILE A1061 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ALA A1063 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ARG A1165 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1107
      removed outlier: 3.763A  pdb=" N   SER A1119 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   GLY A1171 " --> pdb=" O   SER A1057 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   GLY A1059 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ASN A1169 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   ILE A1061 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLY A1167 " --> pdb=" O   ILE A1061 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ALA A1063 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ARG A1165 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   HIS A1170 " --> pdb=" O   SER A1210 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)

    488 hydrogen bonds defined for protein.
    1443 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: 1.42

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2098
        1.34 -     1.46: 1574
        1.46 -     1.58: 3064
        1.58 -     1.69: 0
        1.69 -     1.81: 86
  Bond restraints: 6822
  Sorted by residual:
  bond pdb=" CB  TRP A 862 "
       pdb=" CG  TRP A 862 "
    ideal  model  delta    sigma   weight residual
    1.498  1.566 -0.068 3.10e-02 1.04e+03 4.85e+00
  bond pdb=" C   GLY A1179 "
       pdb=" O   GLY A1179 "
    ideal  model  delta    sigma   weight residual
    1.243  1.227  0.015 9.30e-03 1.16e+04 2.69e+00
  bond pdb=" CA  HIS A 297 "
       pdb=" CB  HIS A 297 "
    ideal  model  delta    sigma   weight residual
    1.528  1.508  0.021 1.56e-02 4.11e+03 1.77e+00
  bond pdb=" CA  TRP A 862 "
       pdb=" CB  TRP A 862 "
    ideal  model  delta    sigma   weight residual
    1.529  1.549 -0.020 1.55e-02 4.16e+03 1.73e+00
  bond pdb=" C   GLY A 861 "
       pdb=" O   GLY A 861 "
    ideal  model  delta    sigma   weight residual
    1.238  1.227  0.012 8.90e-03 1.26e+04 1.68e+00
  ... (remaining 6817 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 8924
        2.00 -     4.00: 248
        4.00 -     6.00: 38
        6.00 -     8.00: 12
        8.00 -    10.00: 4
  Bond angle restraints: 9226
  Sorted by residual:
  angle pdb=" N   GLY A 402 "
        pdb=" CA  GLY A 402 "
        pdb=" C   GLY A 402 "
      ideal   model   delta    sigma   weight residual
     114.90  108.60    6.30 1.54e+00 4.22e-01 1.67e+01
  angle pdb=" C   VAL A 907 "
        pdb=" CA  VAL A 907 "
        pdb=" CB  VAL A 907 "
      ideal   model   delta    sigma   weight residual
     112.05  106.09    5.96 1.46e+00 4.69e-01 1.66e+01
  angle pdb=" CA  GLY A 861 "
        pdb=" C   GLY A 861 "
        pdb=" N   TRP A 862 "
      ideal   model   delta    sigma   weight residual
     115.27  118.28   -3.01 7.60e-01 1.73e+00 1.57e+01
  angle pdb=" N   THR A1181 "
        pdb=" CA  THR A1181 "
        pdb=" C   THR A1181 "
      ideal   model   delta    sigma   weight residual
     113.72  108.45    5.27 1.52e+00 4.33e-01 1.20e+01
  angle pdb=" N   GLY A 222 "
        pdb=" CA  GLY A 222 "
        pdb=" C   GLY A 222 "
      ideal   model   delta    sigma   weight residual
     112.64  108.98    3.66 1.21e+00 6.83e-01 9.14e+00
  ... (remaining 9221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 3586
       17.90 -    35.81: 361
       35.81 -    53.71: 60
       53.71 -    71.62: 8
       71.62 -    89.52: 4
  Dihedral angle restraints: 4019
    sinusoidal: 1572
      harmonic: 2447
  Sorted by residual:
  dihedral pdb=" CA  LYS A1080 "
           pdb=" C   LYS A1080 "
           pdb=" N   GLU A1081 "
           pdb=" CA  GLU A1081 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.04   21.96     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  TYR A 538 "
           pdb=" C   TYR A 538 "
           pdb=" N   LEU A 539 "
           pdb=" CA  LEU A 539 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.25   21.75     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  CYS A 447 "
           pdb=" C   CYS A 447 "
           pdb=" N   VAL A 448 "
           pdb=" CA  VAL A 448 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.56   21.44     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 4016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 675
       0.039 -    0.079: 281
       0.079 -    0.118: 83
       0.118 -    0.157: 17
       0.157 -    0.197: 1
  Chirality restraints: 1057
  Sorted by residual:
  chirality pdb=" CB  ILE A 294 "
            pdb=" CA  ILE A 294 "
            pdb=" CG1 ILE A 294 "
            pdb=" CG2 ILE A 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.65e-01
  chirality pdb=" CA  ILE A1187 "
            pdb=" N   ILE A1187 "
            pdb=" C   ILE A1187 "
            pdb=" CB  ILE A1187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CA  LEU A 875 "
            pdb=" N   LEU A 875 "
            pdb=" C   LEU A 875 "
            pdb=" CB  LEU A 875 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.75e-01
  ... (remaining 1054 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1037 "    0.037 5.00e-02 4.00e+02   5.70e-02 5.19e+00
        pdb=" N   PRO A1038 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A1038 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A1038 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 292 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.95e+00
        pdb=" C   HIS A 292 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   HIS A 292 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A 293 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 226 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.80e+00
        pdb=" C   MET A 226 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   MET A 226 "    0.013 2.00e-02 2.50e+03
        pdb=" N   CYS A 227 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 154
        2.61 -     3.18: 7321
        3.18 -     3.75: 12025
        3.75 -     4.33: 15922
        4.33 -     4.90: 23364
  Nonbonded interactions: 58786
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A1110 "
            pdb=" O   THR A1114 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O   GLN A 220 "
            pdb=" OG  SER A 223 "
     model   vdw
     2.100 3.040
  nonbonded pdb=" O   LEU A 792 "
            pdb=" OG1 THR A 795 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" O   ALA A 783 "
            pdb=" OG  SER A 786 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" O   CYS A 108 "
            pdb=" NE2 GLN A 111 "
     model   vdw
     2.124 3.120
  ... (remaining 58781 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 group one per residue
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:             2.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.260
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
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   0.068   6822  Z= 0.274
  Angle     :  0.873  10.004   9226  Z= 0.508
  Chirality :  0.046   0.197   1057
  Planarity :  0.004   0.057   1145
  Dihedral  : 14.588  89.520   2441
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 38.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.71 %
    Favored  : 88.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.80 (0.22), residues: 828
  helix: -2.77 (0.16), residues: 514
  sheet: -3.05 (0.51), residues: 70
  loop : -3.66 (0.31), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 117 
 TYR   0.018   0.002   TYR A 133 
 PHE   0.022   0.002   PHE A 785 
 TRP   0.016   0.002   TRP A1188 
 HIS   0.012   0.002   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 6822)
  covalent geometry    : angle       0.87274 ( 9226)
  hydrogen bonds       : bond        0.14565 (  462)
  hydrogen bonds       : angle       8.01013 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9472 (t80) cc_final: 0.9234 (t80)
REVERT: A  130 TRP cc_start: 0.8952 (m100) cc_final: 0.8419 (m100)
REVERT: A  145 MET cc_start: 0.9256 (mmt) cc_final: 0.8370 (mpp)
REVERT: A  177 LEU cc_start: 0.9454 (tt) cc_final: 0.9241 (mt)
REVERT: A  227 CYS cc_start: 0.9574 (t) cc_final: 0.9299 (t)
REVERT: A  243 TYR cc_start: 0.8095 (p90) cc_final: 0.7680 (m-80)
REVERT: A  256 PHE cc_start: 0.9098 (t80) cc_final: 0.8814 (t80)
REVERT: A  297 HIS cc_start: 0.9383 (t-90) cc_final: 0.9038 (t-90)
REVERT: A  508 ASP cc_start: 0.9422 (m-30) cc_final: 0.8896 (t70)
REVERT: A  881 TYR cc_start: 0.8979 (m-10) cc_final: 0.8704 (m-10)
REVERT: A  888 PHE cc_start: 0.8968 (p90) cc_final: 0.8686 (p90)
REVERT: A 1145 GLU cc_start: 0.9281 (tt0) cc_final: 0.9043 (tt0)
REVERT: A 1183 LEU cc_start: 0.9224 (tp) cc_final: 0.8957 (tp)
REVERT: A 1187 ILE cc_start: 0.9021 (mm) cc_final: 0.8768 (mm)
REVERT: A 1198 MET cc_start: 0.9259 (mmp) cc_final: 0.8609 (tpp)
REVERT: A 1220 MET cc_start: 0.7106 (mtm) cc_final: 0.6789 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0762
  time to fit residues: 15.5172
Evaluate side-chains
  115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    7.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 356 ASN
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1135 HIS
A1154 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.064966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.048454 restraints weight = 51451.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.049546 restraints weight = 40527.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.050449 restraints weight = 33409.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.051133 restraints weight = 28332.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.051736 restraints weight = 24677.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6822  Z= 0.174
  Angle     :  0.765  12.153   9226  Z= 0.388
  Chirality :  0.045   0.155   1057
  Planarity :  0.005   0.051   1145
  Dihedral  :  5.549  24.067    905
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 20.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.72 %
    Favored  : 93.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.25), residues: 828
  helix: -1.07 (0.19), residues: 536
  sheet: -3.14 (0.42), residues: 88
  loop : -2.99 (0.38), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 542 
 TYR   0.020   0.002   TYR A1083 
 PHE   0.021   0.002   PHE A 897 
 TRP   0.028   0.002   TRP A 995 
 HIS   0.018   0.002   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6822)
  covalent geometry    : angle       0.76453 ( 9226)
  hydrogen bonds       : bond        0.04840 (  462)
  hydrogen bonds       : angle       5.72804 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.9597 (mmt) cc_final: 0.9288 (mpp)
REVERT: A  177 LEU cc_start: 0.9501 (tt) cc_final: 0.9279 (mt)
REVERT: A  180 THR cc_start: 0.9698 (t) cc_final: 0.9453 (t)
REVERT: A  192 PHE cc_start: 0.5564 (t80) cc_final: 0.5066 (t80)
REVERT: A  227 CYS cc_start: 0.9392 (t) cc_final: 0.8928 (t)
REVERT: A  234 LEU cc_start: 0.9496 (tt) cc_final: 0.9031 (tt)
REVERT: A  243 TYR cc_start: 0.7979 (p90) cc_final: 0.7538 (m-80)
REVERT: A  256 PHE cc_start: 0.9177 (t80) cc_final: 0.8911 (t80)
REVERT: A  297 HIS cc_start: 0.9342 (t-90) cc_final: 0.9017 (t-90)
REVERT: A  508 ASP cc_start: 0.9404 (m-30) cc_final: 0.8955 (t70)
REVERT: A  881 TYR cc_start: 0.8744 (m-10) cc_final: 0.8471 (m-10)
REVERT: A  909 TYR cc_start: 0.9050 (m-80) cc_final: 0.8825 (m-10)
REVERT: A  987 PHE cc_start: 0.9543 (m-10) cc_final: 0.9162 (m-10)
REVERT: A 1001 PHE cc_start: 0.9182 (m-10) cc_final: 0.8898 (m-10)
REVERT: A 1083 TYR cc_start: 0.8670 (m-80) cc_final: 0.8345 (m-80)
REVERT: A 1198 MET cc_start: 0.9183 (mmp) cc_final: 0.8605 (ttm)
REVERT: A 1220 MET cc_start: 0.7351 (mtm) cc_final: 0.7054 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0628
  time to fit residues: 12.5052
Evaluate side-chains
  108 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 ASN
** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.066761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.050095 restraints weight = 50212.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.051009 restraints weight = 40166.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.051951 restraints weight = 34011.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.052698 restraints weight = 29157.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.053215 restraints weight = 25424.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6822  Z= 0.154
  Angle     :  0.728  11.072   9226  Z= 0.368
  Chirality :  0.044   0.187   1057
  Planarity :  0.004   0.052   1145
  Dihedral  :  5.246  22.141    905
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 17.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.04 %
    Favored  : 93.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.27), residues: 828
  helix: -0.11 (0.21), residues: 536
  sheet: -3.10 (0.43), residues: 88
  loop : -2.59 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 305 
 TYR   0.018   0.002   TYR A 445 
 PHE   0.039   0.002   PHE A 184 
 TRP   0.036   0.002   TRP A 130 
 HIS   0.010   0.002   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6822)
  covalent geometry    : angle       0.72779 ( 9226)
  hydrogen bonds       : bond        0.04443 (  462)
  hydrogen bonds       : angle       5.26521 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.9544 (mmt) cc_final: 0.9328 (mpp)
REVERT: A  177 LEU cc_start: 0.9499 (tt) cc_final: 0.9273 (mt)
REVERT: A  180 THR cc_start: 0.9762 (t) cc_final: 0.9457 (t)
REVERT: A  192 PHE cc_start: 0.6023 (t80) cc_final: 0.5592 (t80)
REVERT: A  227 CYS cc_start: 0.9376 (t) cc_final: 0.9090 (t)
REVERT: A  243 TYR cc_start: 0.7922 (p90) cc_final: 0.7522 (m-80)
REVERT: A  256 PHE cc_start: 0.9194 (t80) cc_final: 0.8905 (t80)
REVERT: A  297 HIS cc_start: 0.9345 (t-90) cc_final: 0.9032 (t-90)
REVERT: A  305 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8599 (tpp80)
REVERT: A  508 ASP cc_start: 0.9425 (m-30) cc_final: 0.8998 (t70)
REVERT: A  545 MET cc_start: 0.8535 (tpt) cc_final: 0.8323 (tpt)
REVERT: A  793 LEU cc_start: 0.9623 (mt) cc_final: 0.9422 (mt)
REVERT: A  881 TYR cc_start: 0.8763 (m-10) cc_final: 0.8466 (m-10)
REVERT: A  985 LEU cc_start: 0.8978 (mt) cc_final: 0.8767 (mt)
REVERT: A  987 PHE cc_start: 0.9528 (m-10) cc_final: 0.9074 (m-10)
REVERT: A 1001 PHE cc_start: 0.9092 (m-10) cc_final: 0.8884 (m-10)
REVERT: A 1016 ASP cc_start: 0.9368 (t0) cc_final: 0.9092 (p0)
REVERT: A 1083 TYR cc_start: 0.8774 (m-80) cc_final: 0.8418 (m-80)
REVERT: A 1198 MET cc_start: 0.9114 (mmp) cc_final: 0.8584 (ttm)
REVERT: A 1220 MET cc_start: 0.7477 (mtm) cc_final: 0.7243 (mtm)
  outliers start: 2
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0611
  time to fit residues: 12.5040
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
A 883 HIS
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1237 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.067896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.050661 restraints weight = 48623.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.051687 restraints weight = 39489.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.052495 restraints weight = 33266.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.053187 restraints weight = 29069.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.053702 restraints weight = 25776.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6822  Z= 0.148
  Angle     :  0.716   9.383   9226  Z= 0.365
  Chirality :  0.044   0.226   1057
  Planarity :  0.005   0.064   1145
  Dihedral  :  5.167  22.043    905
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 17.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.28), residues: 828
  helix:  0.40 (0.21), residues: 527
  sheet: -3.28 (0.39), residues: 104
  loop : -2.31 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 920 
 TYR   0.013   0.002   TYR A 538 
 PHE   0.041   0.002   PHE A 184 
 TRP   0.017   0.001   TRP A 130 
 HIS   0.006   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6822)
  covalent geometry    : angle       0.71636 ( 9226)
  hydrogen bonds       : bond        0.04315 (  462)
  hydrogen bonds       : angle       5.00758 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.9567 (mmt) cc_final: 0.9363 (mpp)
REVERT: A  192 PHE cc_start: 0.6131 (t80) cc_final: 0.5749 (t80)
REVERT: A  227 CYS cc_start: 0.9342 (t) cc_final: 0.9106 (t)
REVERT: A  243 TYR cc_start: 0.7860 (p90) cc_final: 0.7446 (m-80)
REVERT: A  256 PHE cc_start: 0.9265 (t80) cc_final: 0.9022 (t80)
REVERT: A  297 HIS cc_start: 0.9232 (t-90) cc_final: 0.8992 (t-90)
REVERT: A  508 ASP cc_start: 0.9405 (m-30) cc_final: 0.8984 (t70)
REVERT: A  545 MET cc_start: 0.8563 (tpt) cc_final: 0.8355 (tpt)
REVERT: A  881 TYR cc_start: 0.8830 (m-10) cc_final: 0.8508 (m-10)
REVERT: A  985 LEU cc_start: 0.8970 (mt) cc_final: 0.8745 (mt)
REVERT: A  987 PHE cc_start: 0.9505 (m-10) cc_final: 0.9057 (m-80)
REVERT: A 1001 PHE cc_start: 0.8973 (m-10) cc_final: 0.8741 (m-10)
REVERT: A 1016 ASP cc_start: 0.9408 (t0) cc_final: 0.9128 (p0)
REVERT: A 1083 TYR cc_start: 0.8864 (m-80) cc_final: 0.8408 (m-10)
REVERT: A 1198 MET cc_start: 0.9032 (mmp) cc_final: 0.8346 (ttt)
REVERT: A 1220 MET cc_start: 0.7549 (mtm) cc_final: 0.7317 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0567
  time to fit residues: 11.7205
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 42 optimal weight:    0.4980
   chunk 77 optimal weight:    0.2980
   chunk 70 optimal weight:    0.0870
   chunk 63 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 39 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
** A 420 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 = 0.3550 r_free = 0.3550 target = 0.070749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.052538 restraints weight = 48386.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.053599 restraints weight = 39371.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.054520 restraints weight = 33509.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.055234 restraints weight = 28949.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.055729 restraints weight = 25651.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.4650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6822  Z= 0.129
  Angle     :  0.704   9.620   9226  Z= 0.349
  Chirality :  0.043   0.216   1057
  Planarity :  0.004   0.049   1145
  Dihedral  :  4.859  21.003    905
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.47 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.29), residues: 828
  helix:  0.78 (0.22), residues: 538
  sheet: -2.81 (0.42), residues: 101
  loop : -2.45 (0.41), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1148 
 TYR   0.019   0.001   TYR A 445 
 PHE   0.034   0.002   PHE A 224 
 TRP   0.015   0.001   TRP A 130 
 HIS   0.004   0.001   HIS A1010 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6822)
  covalent geometry    : angle       0.70449 ( 9226)
  hydrogen bonds       : bond        0.03978 (  462)
  hydrogen bonds       : angle       4.64171 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9434 (t80) cc_final: 0.8882 (t80)
REVERT: A  192 PHE cc_start: 0.6165 (t80) cc_final: 0.5774 (t80)
REVERT: A  227 CYS cc_start: 0.9322 (t) cc_final: 0.9120 (t)
REVERT: A  243 TYR cc_start: 0.7789 (p90) cc_final: 0.7315 (m-80)
REVERT: A  298 LEU cc_start: 0.9751 (mm) cc_final: 0.9415 (mm)
REVERT: A  508 ASP cc_start: 0.9413 (m-30) cc_final: 0.9004 (t70)
REVERT: A  545 MET cc_start: 0.8656 (tpt) cc_final: 0.8425 (tpt)
REVERT: A  987 PHE cc_start: 0.9475 (m-10) cc_final: 0.8990 (m-80)
REVERT: A  995 TRP cc_start: 0.8168 (t60) cc_final: 0.7835 (t60)
REVERT: A 1016 ASP cc_start: 0.9434 (t0) cc_final: 0.9168 (p0)
REVERT: A 1198 MET cc_start: 0.8998 (mmp) cc_final: 0.8314 (ttt)
REVERT: A 1220 MET cc_start: 0.7677 (mtm) cc_final: 0.7073 (ptp)
  outliers start: 1
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0665
  time to fit residues: 14.1149
Evaluate side-chains
  120 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 76 optimal weight:   20.0000
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1008 HIS
A1170 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.070528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.053174 restraints weight = 49946.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.054254 restraints weight = 40916.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.054985 restraints weight = 34710.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.055757 restraints weight = 30613.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.056291 restraints weight = 27127.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6822  Z= 0.149
  Angle     :  0.754   9.433   9226  Z= 0.378
  Chirality :  0.044   0.203   1057
  Planarity :  0.004   0.058   1145
  Dihedral  :  4.836  21.261    905
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.19 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.28), residues: 828
  helix:  0.69 (0.22), residues: 530
  sheet: -2.65 (0.41), residues: 113
  loop : -2.15 (0.43), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1148 
 TYR   0.018   0.002   TYR A 881 
 PHE   0.051   0.002   PHE A 798 
 TRP   0.008   0.001   TRP A 510 
 HIS   0.017   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6822)
  covalent geometry    : angle       0.75412 ( 9226)
  hydrogen bonds       : bond        0.04170 (  462)
  hydrogen bonds       : angle       4.75182 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 PHE cc_start: 0.6090 (t80) cc_final: 0.5697 (t80)
REVERT: A  243 TYR cc_start: 0.7675 (p90) cc_final: 0.7253 (m-80)
REVERT: A  508 ASP cc_start: 0.9403 (m-30) cc_final: 0.9099 (t70)
REVERT: A  545 MET cc_start: 0.8653 (tpt) cc_final: 0.8401 (tpt)
REVERT: A  919 MET cc_start: 0.8590 (mmt) cc_final: 0.8372 (mmt)
REVERT: A  987 PHE cc_start: 0.9477 (m-10) cc_final: 0.8975 (m-80)
REVERT: A  995 TRP cc_start: 0.8192 (t60) cc_final: 0.7869 (t60)
REVERT: A 1001 PHE cc_start: 0.9168 (m-10) cc_final: 0.8895 (m-10)
REVERT: A 1016 ASP cc_start: 0.9452 (t0) cc_final: 0.9164 (p0)
REVERT: A 1083 TYR cc_start: 0.8687 (m-10) cc_final: 0.8479 (m-10)
REVERT: A 1170 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7649 (p90)
REVERT: A 1198 MET cc_start: 0.8952 (mmp) cc_final: 0.8332 (ttm)
REVERT: A 1215 ARG cc_start: 0.9427 (ptt-90) cc_final: 0.9168 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7642 (mtm) cc_final: 0.7329 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0629
  time to fit residues: 12.5335
Evaluate side-chains
  113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 41 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   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 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 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 = 0.3565 r_free = 0.3565 target = 0.071933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.054574 restraints weight = 48768.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.055683 restraints weight = 39817.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.056370 restraints weight = 33559.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.057213 restraints weight = 29474.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.057816 restraints weight = 26104.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.5617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6822  Z= 0.138
  Angle     :  0.766   9.845   9226  Z= 0.381
  Chirality :  0.044   0.175   1057
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.779  20.361    905
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.29), residues: 828
  helix:  0.71 (0.22), residues: 528
  sheet: -2.54 (0.44), residues: 106
  loop : -2.04 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 920 
 TYR   0.020   0.002   TYR A1102 
 PHE   0.040   0.002   PHE A 798 
 TRP   0.008   0.001   TRP A 995 
 HIS   0.012   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6822)
  covalent geometry    : angle       0.76646 ( 9226)
  hydrogen bonds       : bond        0.04048 (  462)
  hydrogen bonds       : angle       4.61698 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 PHE cc_start: 0.6175 (t80) cc_final: 0.5779 (t80)
REVERT: A  243 TYR cc_start: 0.7692 (p90) cc_final: 0.7230 (m-80)
REVERT: A  499 ILE cc_start: 0.8696 (tp) cc_final: 0.8451 (tp)
REVERT: A  508 ASP cc_start: 0.9400 (m-30) cc_final: 0.9097 (t70)
REVERT: A  520 MET cc_start: 0.7280 (ptt) cc_final: 0.6746 (ptt)
REVERT: A  545 MET cc_start: 0.8688 (tpt) cc_final: 0.8429 (tpt)
REVERT: A  919 MET cc_start: 0.8519 (mmt) cc_final: 0.8280 (mmt)
REVERT: A  987 PHE cc_start: 0.9476 (m-10) cc_final: 0.8954 (m-80)
REVERT: A  995 TRP cc_start: 0.8151 (t60) cc_final: 0.7881 (t60)
REVERT: A 1001 PHE cc_start: 0.9124 (m-10) cc_final: 0.8844 (m-10)
REVERT: A 1016 ASP cc_start: 0.9426 (t0) cc_final: 0.9149 (p0)
REVERT: A 1083 TYR cc_start: 0.8589 (m-10) cc_final: 0.8381 (m-80)
REVERT: A 1110 THR cc_start: 0.9074 (p) cc_final: 0.8773 (p)
REVERT: A 1188 TRP cc_start: 0.8863 (p90) cc_final: 0.8385 (p90)
REVERT: A 1198 MET cc_start: 0.8936 (mmp) cc_final: 0.8275 (ttm)
REVERT: A 1215 ARG cc_start: 0.9404 (ptt-90) cc_final: 0.9125 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7661 (mtm) cc_final: 0.7230 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0685
  time to fit residues: 13.2061
Evaluate side-chains
  120 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 75 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
A 356 ASN
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.072534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.054859 restraints weight = 48063.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.055959 restraints weight = 39277.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.056875 restraints weight = 33292.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.057508 restraints weight = 28828.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.058199 restraints weight = 25669.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.5879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6822  Z= 0.134
  Angle     :  0.756   9.501   9226  Z= 0.378
  Chirality :  0.044   0.169   1057
  Planarity :  0.004   0.064   1145
  Dihedral  :  4.720  20.766    905
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.29), residues: 828
  helix:  0.79 (0.22), residues: 526
  sheet: -2.37 (0.44), residues: 106
  loop : -2.01 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1148 
 TYR   0.024   0.001   TYR A 445 
 PHE   0.034   0.002   PHE A 798 
 TRP   0.007   0.001   TRP A 130 
 HIS   0.013   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6822)
  covalent geometry    : angle       0.75638 ( 9226)
  hydrogen bonds       : bond        0.03983 (  462)
  hydrogen bonds       : angle       4.58338 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.260 
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  243 TYR cc_start: 0.7677 (p90) cc_final: 0.7221 (m-80)
REVERT: A  508 ASP cc_start: 0.9269 (m-30) cc_final: 0.9005 (t70)
REVERT: A  545 MET cc_start: 0.8660 (tpt) cc_final: 0.8381 (tpt)
REVERT: A  919 MET cc_start: 0.8600 (mmt) cc_final: 0.8390 (mmt)
REVERT: A  987 PHE cc_start: 0.9467 (m-10) cc_final: 0.8926 (m-80)
REVERT: A  996 PHE cc_start: 0.9045 (m-80) cc_final: 0.8701 (m-80)
REVERT: A 1001 PHE cc_start: 0.9157 (m-10) cc_final: 0.8888 (m-10)
REVERT: A 1016 ASP cc_start: 0.9415 (t0) cc_final: 0.9141 (p0)
REVERT: A 1083 TYR cc_start: 0.8607 (m-10) cc_final: 0.8396 (m-80)
REVERT: A 1110 THR cc_start: 0.9120 (p) cc_final: 0.8852 (p)
REVERT: A 1188 TRP cc_start: 0.8836 (p90) cc_final: 0.8317 (p90)
REVERT: A 1198 MET cc_start: 0.8937 (mmp) cc_final: 0.8267 (ttm)
REVERT: A 1220 MET cc_start: 0.7610 (mtm) cc_final: 0.7201 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0657
  time to fit residues: 13.2343
Evaluate side-chains
  113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 40 optimal weight:   10.0000
   chunk 30 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0870
   chunk 50 optimal weight:    4.9990
   overall best weight:    1.3162

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

Flipped N/Q/H residues before XYZ refinement:
A 303 GLN
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1170 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.071271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.053652 restraints weight = 48069.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.054761 restraints weight = 39357.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.055519 restraints weight = 33212.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.056312 restraints weight = 29269.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.056895 restraints weight = 25975.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.6015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   6822  Z= 0.142
  Angle     :  0.765   9.480   9226  Z= 0.389
  Chirality :  0.044   0.167   1057
  Planarity :  0.004   0.043   1145
  Dihedral  :  4.684  21.306    905
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.29), residues: 828
  helix:  0.72 (0.22), residues: 526
  sheet: -2.10 (0.51), residues: 81
  loop : -2.19 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1148 
 TYR   0.012   0.001   TYR A 538 
 PHE   0.041   0.002   PHE A 224 
 TRP   0.008   0.001   TRP A 130 
 HIS   0.012   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6822)
  covalent geometry    : angle       0.76486 ( 9226)
  hydrogen bonds       : bond        0.04036 (  462)
  hydrogen bonds       : angle       4.65847 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 TYR cc_start: 0.7613 (p90) cc_final: 0.7152 (m-80)
REVERT: A  499 ILE cc_start: 0.8642 (tp) cc_final: 0.8409 (tp)
REVERT: A  508 ASP cc_start: 0.9266 (m-30) cc_final: 0.8991 (t70)
REVERT: A  545 MET cc_start: 0.8700 (tpt) cc_final: 0.8406 (tpt)
REVERT: A  987 PHE cc_start: 0.9464 (m-10) cc_final: 0.8916 (m-80)
REVERT: A  996 PHE cc_start: 0.9067 (m-80) cc_final: 0.8717 (m-80)
REVERT: A 1001 PHE cc_start: 0.9178 (m-10) cc_final: 0.8836 (m-10)
REVERT: A 1016 ASP cc_start: 0.9421 (t0) cc_final: 0.9143 (p0)
REVERT: A 1083 TYR cc_start: 0.8640 (m-10) cc_final: 0.8398 (m-10)
REVERT: A 1110 THR cc_start: 0.9135 (p) cc_final: 0.8919 (p)
REVERT: A 1188 TRP cc_start: 0.8835 (p90) cc_final: 0.8285 (p90)
REVERT: A 1198 MET cc_start: 0.8918 (mmp) cc_final: 0.8236 (ttm)
REVERT: A 1215 ARG cc_start: 0.9415 (ptt-90) cc_final: 0.9101 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7553 (mtm) cc_final: 0.7068 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0602
  time to fit residues: 11.9606
Evaluate side-chains
  114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 80 optimal weight:    8.9990
   chunk 32 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
A 420 ASN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.069716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.052344 restraints weight = 49530.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.053399 restraints weight = 40418.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.054284 restraints weight = 34106.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.054892 restraints weight = 29483.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.055510 restraints weight = 26222.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.6024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   6822  Z= 0.169
  Angle     :  0.796   9.888   9226  Z= 0.411
  Chirality :  0.045   0.178   1057
  Planarity :  0.004   0.045   1145
  Dihedral  :  4.882  22.710    905
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 17.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.28), residues: 828
  helix:  0.44 (0.22), residues: 526
  sheet: -2.51 (0.43), residues: 100
  loop : -2.04 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1148 
 TYR   0.011   0.002   TYR A 122 
 PHE   0.037   0.002   PHE A 184 
 TRP   0.014   0.002   TRP A 130 
 HIS   0.015   0.002   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 6822)
  covalent geometry    : angle       0.79630 ( 9226)
  hydrogen bonds       : bond        0.04372 (  462)
  hydrogen bonds       : angle       4.83139 ( 1443)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9583 (t80) cc_final: 0.9266 (t80)
REVERT: A  184 PHE cc_start: 0.9434 (m-80) cc_final: 0.9166 (m-80)
REVERT: A  229 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8992 (mt-10)
REVERT: A  243 TYR cc_start: 0.7557 (p90) cc_final: 0.7134 (m-80)
REVERT: A  508 ASP cc_start: 0.9302 (m-30) cc_final: 0.9015 (t70)
REVERT: A  545 MET cc_start: 0.8711 (tpt) cc_final: 0.8421 (tpt)
REVERT: A  987 PHE cc_start: 0.9468 (m-10) cc_final: 0.8928 (m-80)
REVERT: A  995 TRP cc_start: 0.8155 (t60) cc_final: 0.7921 (t60)
REVERT: A 1001 PHE cc_start: 0.9189 (m-10) cc_final: 0.8821 (m-10)
REVERT: A 1016 ASP cc_start: 0.9412 (t0) cc_final: 0.9136 (p0)
REVERT: A 1083 TYR cc_start: 0.8610 (m-10) cc_final: 0.8385 (m-10)
REVERT: A 1188 TRP cc_start: 0.8823 (p90) cc_final: 0.8263 (p90)
REVERT: A 1198 MET cc_start: 0.8863 (mmp) cc_final: 0.8080 (ttm)
REVERT: A 1220 MET cc_start: 0.7637 (mtm) cc_final: 0.7238 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0579
  time to fit residues: 11.0669
Evaluate side-chains
  109 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   chunk 13 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 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 = 0.3550 r_free = 0.3550 target = 0.070337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.052600 restraints weight = 46067.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.053660 restraints weight = 37853.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.054540 restraints weight = 32085.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.055267 restraints weight = 27927.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.055791 restraints weight = 24760.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.6231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6822  Z= 0.146
  Angle     :  0.775   9.620   9226  Z= 0.395
  Chirality :  0.045   0.174   1057
  Planarity :  0.004   0.043   1145
  Dihedral  :  4.818  21.687    905
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 16.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.29), residues: 828
  helix:  0.58 (0.22), residues: 526
  sheet: -2.15 (0.50), residues: 81
  loop : -2.20 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1148 
 TYR   0.012   0.001   TYR A 538 
 PHE   0.040   0.002   PHE A 184 
 TRP   0.016   0.002   TRP A1159 
 HIS   0.010   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6822)
  covalent geometry    : angle       0.77530 ( 9226)
  hydrogen bonds       : bond        0.04185 (  462)
  hydrogen bonds       : angle       4.78304 ( 1443)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1262.13 seconds
wall clock time: 22 minutes 36.77 seconds (1356.77 seconds total)