Starting phenix.real_space_refine
on Tue Feb 11 23:09:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pd4_13330/02_2025/7pd4_13330.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pd4_13330/02_2025/7pd4_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_13330/02_2025/7pd4_13330.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pd4_13330/02_2025/7pd4_13330.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pd4_13330/02_2025/7pd4_13330.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pd4_13330/02_2025/7pd4_13330.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.38, per 1000 atoms: 0.66
  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: 1.82
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.79
  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: 2.60

  Time building geometry restraints manager: 2.13 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.670
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.130
-------------------------------------------------------------------------------
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= 0.330
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.016   0.002   TRP A1188 
 HIS   0.012   0.002   HIS A 297 
 PHE   0.022   0.002   PHE A 785 
 TYR   0.018   0.002   TYR A 133 
 ARG   0.003   0.001   ARG A 117 

*********************** 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  : 0.724 
Fit side-chains
   revert: symmetry clash
   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: 0.9230 (mt)
REVERT: A  227 CYS cc_start: 0.9574 (t) cc_final: 0.9300 (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: 0.9037 (t-90)
REVERT: A  508 ASP cc_start: 0.9422 (m-30) cc_final: 0.8904 (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: 0.9044 (tt0)
REVERT: A 1183 LEU cc_start: 0.9224 (tp) cc_final: 0.8956 (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: 0.8903 (mmm)
REVERT: A 1220 MET cc_start: 0.7106 (mtm) cc_final: 0.6790 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1716
  time to fit residues: 34.2651
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  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 65 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    9.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1135 HIS
A1154 ASN
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.064435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.048112 restraints weight = 50986.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.049199 restraints weight = 40111.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.050059 restraints weight = 32900.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2615

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= 0.247
  Angle     :  0.779  12.462   9226  Z= 0.395
  Chirality :  0.046   0.157   1057
  Planarity :  0.005   0.056   1145
  Dihedral  :  5.621  24.331    905
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 21.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  7.13 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.25), residues: 828
  helix: -1.14 (0.19), residues: 536
  sheet: -3.14 (0.43), residues: 88
  loop : -2.98 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 995 
 HIS   0.019   0.002   HIS A 292 
 PHE   0.025   0.002   PHE A 897 
 TYR   0.022   0.002   TYR A1083 
 ARG   0.006   0.001   ARG A1215 

*********************** 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
  135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.9604 (mmt) cc_final: 0.9294 (mpp)
REVERT: A  177 LEU cc_start: 0.9510 (tt) cc_final: 0.9286 (mt)
REVERT: A  227 CYS cc_start: 0.9357 (t) cc_final: 0.8922 (t)
REVERT: A  243 TYR cc_start: 0.7997 (p90) cc_final: 0.7575 (m-80)
REVERT: A  256 PHE cc_start: 0.9189 (t80) cc_final: 0.8898 (t80)
REVERT: A  297 HIS cc_start: 0.9328 (t-90) cc_final: 0.8983 (t-90)
REVERT: A  508 ASP cc_start: 0.9413 (m-30) cc_final: 0.8979 (t70)
REVERT: A  881 TYR cc_start: 0.8772 (m-10) cc_final: 0.8484 (m-10)
REVERT: A  987 PHE cc_start: 0.9544 (m-10) cc_final: 0.9141 (m-10)
REVERT: A 1083 TYR cc_start: 0.8672 (m-80) cc_final: 0.8452 (m-10)
REVERT: A 1198 MET cc_start: 0.9177 (mmp) cc_final: 0.8620 (ttm)
REVERT: A 1220 MET cc_start: 0.7344 (mtm) cc_final: 0.7046 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1551
  time to fit residues: 29.2532
Evaluate side-chains
  104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 12 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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**
** A1170 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 = 0.3475 r_free = 0.3475 target = 0.066077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.049502 restraints weight = 50274.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.050613 restraints weight = 39752.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.051514 restraints weight = 32799.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.3444

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= 0.219
  Angle     :  0.731  11.352   9226  Z= 0.371
  Chirality :  0.044   0.187   1057
  Planarity :  0.005   0.051   1145
  Dihedral  :  5.256  21.840    905
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.31 %
    Favored  : 93.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.27), residues: 828
  helix: -0.16 (0.21), residues: 533
  sheet: -3.15 (0.44), residues: 90
  loop : -2.62 (0.41), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 130 
 HIS   0.009   0.002   HIS A 292 
 PHE   0.036   0.002   PHE A 184 
 TYR   0.017   0.002   TYR A 445 
 ARG   0.010   0.001   ARG A1148 

*********************** 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  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.9559 (mmt) cc_final: 0.9346 (mpp)
REVERT: A  177 LEU cc_start: 0.9524 (tt) cc_final: 0.9292 (mt)
REVERT: A  227 CYS cc_start: 0.9363 (t) cc_final: 0.9029 (t)
REVERT: A  243 TYR cc_start: 0.7928 (p90) cc_final: 0.7491 (m-80)
REVERT: A  256 PHE cc_start: 0.9231 (t80) cc_final: 0.8888 (t80)
REVERT: A  297 HIS cc_start: 0.9311 (t-90) cc_final: 0.9001 (t-90)
REVERT: A  305 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8551 (tpp80)
REVERT: A  423 PHE cc_start: 0.9493 (m-10) cc_final: 0.9293 (m-80)
REVERT: A  508 ASP cc_start: 0.9436 (m-30) cc_final: 0.9031 (t70)
REVERT: A  545 MET cc_start: 0.8551 (tpt) cc_final: 0.8324 (tpt)
REVERT: A  881 TYR cc_start: 0.8838 (m-10) cc_final: 0.8548 (m-10)
REVERT: A  987 PHE cc_start: 0.9534 (m-10) cc_final: 0.9071 (m-10)
REVERT: A 1001 PHE cc_start: 0.9150 (m-10) cc_final: 0.8911 (m-10)
REVERT: A 1016 ASP cc_start: 0.9364 (t0) cc_final: 0.9082 (p0)
REVERT: A 1083 TYR cc_start: 0.8766 (m-80) cc_final: 0.8477 (m-10)
REVERT: A 1198 MET cc_start: 0.9087 (mmp) cc_final: 0.8568 (ttm)
REVERT: A 1220 MET cc_start: 0.7413 (mtm) cc_final: 0.7166 (mtm)
  outliers start: 2
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1553
  time to fit residues: 30.6870
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  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 77 optimal weight:    8.9990
   chunk 80 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 883 HIS
A1237 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.068365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.050266 restraints weight = 48781.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.051330 restraints weight = 39752.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.051992 restraints weight = 33497.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.4238

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= 0.181
  Angle     :  0.698   9.716   9226  Z= 0.353
  Chirality :  0.044   0.186   1057
  Planarity :  0.004   0.048   1145
  Dihedral  :  4.969  20.946    905
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.28), residues: 828
  helix:  0.50 (0.22), residues: 536
  sheet: -2.94 (0.40), residues: 103
  loop : -2.39 (0.44), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 995 
 HIS   0.005   0.001   HIS A 292 
 PHE   0.043   0.002   PHE A 798 
 TYR   0.014   0.002   TYR A 538 
 ARG   0.007   0.001   ARG A1148 

*********************** 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
  144 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 THR cc_start: 0.9751 (p) cc_final: 0.9440 (t)
REVERT: A  220 GLN cc_start: 0.9127 (pm20) cc_final: 0.8902 (pm20)
REVERT: A  227 CYS cc_start: 0.9367 (t) cc_final: 0.9041 (t)
REVERT: A  243 TYR cc_start: 0.7872 (p90) cc_final: 0.7453 (m-80)
REVERT: A  256 PHE cc_start: 0.9261 (t80) cc_final: 0.8952 (t80)
REVERT: A  297 HIS cc_start: 0.9192 (t-90) cc_final: 0.8951 (t-90)
REVERT: A  423 PHE cc_start: 0.9475 (m-10) cc_final: 0.9182 (m-80)
REVERT: A  508 ASP cc_start: 0.9395 (m-30) cc_final: 0.9025 (t70)
REVERT: A  520 MET cc_start: 0.7880 (ptt) cc_final: 0.7309 (ptp)
REVERT: A  888 PHE cc_start: 0.9096 (p90) cc_final: 0.8883 (p90)
REVERT: A  987 PHE cc_start: 0.9502 (m-10) cc_final: 0.9056 (m-80)
REVERT: A 1016 ASP cc_start: 0.9432 (t0) cc_final: 0.9162 (p0)
REVERT: A 1083 TYR cc_start: 0.8924 (m-80) cc_final: 0.8413 (m-10)
REVERT: A 1146 MET cc_start: 0.9550 (mmt) cc_final: 0.9333 (mmm)
REVERT: A 1198 MET cc_start: 0.9032 (mmp) cc_final: 0.8332 (ttt)
REVERT: A 1215 ARG cc_start: 0.9436 (ptt-90) cc_final: 0.9177 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7649 (mtm) cc_final: 0.7015 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1543
  time to fit residues: 31.1801
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  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    0.1980
   chunk 64 optimal weight:    8.9990
   chunk 69 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 28 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1010 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.068855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.051044 restraints weight = 48521.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.052104 restraints weight = 39750.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.052891 restraints weight = 33763.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.4778

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= 0.184
  Angle     :  0.722   9.433   9226  Z= 0.358
  Chirality :  0.044   0.217   1057
  Planarity :  0.005   0.052   1145
  Dihedral  :  4.826  20.641    905
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.28), residues: 828
  helix:  0.63 (0.21), residues: 538
  sheet: -3.02 (0.41), residues: 100
  loop : -2.39 (0.42), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 995 
 HIS   0.005   0.001   HIS A 297 
 PHE   0.023   0.002   PHE A 798 
 TYR   0.017   0.002   TYR A 881 
 ARG   0.008   0.000   ARG A1148 

*********************** 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
  147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 THR cc_start: 0.9737 (p) cc_final: 0.9483 (p)
REVERT: A  184 PHE cc_start: 0.9507 (m-80) cc_final: 0.9270 (m-80)
REVERT: A  227 CYS cc_start: 0.9391 (t) cc_final: 0.9041 (t)
REVERT: A  243 TYR cc_start: 0.7853 (p90) cc_final: 0.7447 (m-80)
REVERT: A  256 PHE cc_start: 0.9201 (t80) cc_final: 0.8993 (t80)
REVERT: A  297 HIS cc_start: 0.9202 (t-90) cc_final: 0.8890 (t-90)
REVERT: A  298 LEU cc_start: 0.9740 (mm) cc_final: 0.9461 (mm)
REVERT: A  423 PHE cc_start: 0.9464 (m-10) cc_final: 0.9224 (m-80)
REVERT: A  508 ASP cc_start: 0.9408 (m-30) cc_final: 0.9151 (t70)
REVERT: A  987 PHE cc_start: 0.9491 (m-10) cc_final: 0.9002 (m-80)
REVERT: A 1001 PHE cc_start: 0.9305 (m-10) cc_final: 0.8725 (m-10)
REVERT: A 1016 ASP cc_start: 0.9436 (t0) cc_final: 0.9158 (p0)
REVERT: A 1083 TYR cc_start: 0.8936 (m-80) cc_final: 0.8687 (m-10)
REVERT: A 1198 MET cc_start: 0.9008 (mmp) cc_final: 0.8330 (ttt)
REVERT: A 1215 ARG cc_start: 0.9431 (ptt-90) cc_final: 0.9167 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7669 (mtm) cc_final: 0.7044 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1568
  time to fit residues: 31.8378
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  : 0.784 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 12 optimal weight:    0.3980
   chunk 43 optimal weight:    5.9990
   chunk 71 optimal weight:   40.0000
   chunk 79 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    4.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
A 356 ASN
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
A1170 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.064710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.048230 restraints weight = 53813.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.049190 restraints weight = 43919.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.049836 restraints weight = 36989.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.4798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   6822  Z= 0.326
  Angle     :  0.814   9.369   9226  Z= 0.421
  Chirality :  0.047   0.177   1057
  Planarity :  0.005   0.066   1145
  Dihedral  :  5.317  21.036    905
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 24.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.12 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.27), residues: 828
  helix:  0.01 (0.21), residues: 527
  sheet: -2.85 (0.42), residues: 103
  loop : -2.26 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP A 995 
 HIS   0.011   0.002   HIS A 297 
 PHE   0.026   0.002   PHE A 121 
 TYR   0.017   0.002   TYR A1009 
 ARG   0.017   0.001   ARG A1148 

*********************** 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
  134 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9429 (t80) cc_final: 0.9137 (t80)
REVERT: A  180 THR cc_start: 0.9758 (p) cc_final: 0.9541 (p)
REVERT: A  184 PHE cc_start: 0.9581 (m-10) cc_final: 0.9337 (m-80)
REVERT: A  227 CYS cc_start: 0.9397 (t) cc_final: 0.9141 (t)
REVERT: A  243 TYR cc_start: 0.7717 (p90) cc_final: 0.7384 (m-80)
REVERT: A  297 HIS cc_start: 0.9376 (t-90) cc_final: 0.9071 (t-90)
REVERT: A  508 ASP cc_start: 0.9405 (m-30) cc_final: 0.9158 (t70)
REVERT: A  520 MET cc_start: 0.7912 (ptt) cc_final: 0.7295 (ptt)
REVERT: A  987 PHE cc_start: 0.9537 (m-10) cc_final: 0.9025 (m-80)
REVERT: A 1001 PHE cc_start: 0.8957 (m-10) cc_final: 0.8628 (m-10)
REVERT: A 1016 ASP cc_start: 0.9422 (t0) cc_final: 0.9131 (p0)
REVERT: A 1083 TYR cc_start: 0.9032 (m-80) cc_final: 0.8430 (m-80)
REVERT: A 1157 MET cc_start: 0.8619 (ptm) cc_final: 0.8348 (ptt)
REVERT: A 1170 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.7705 (p90)
REVERT: A 1198 MET cc_start: 0.8847 (mmp) cc_final: 0.8147 (ttm)
REVERT: A 1220 MET cc_start: 0.7570 (mtm) cc_final: 0.7309 (mtp)
  outliers start: 2
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1385
  time to fit residues: 27.2131
Evaluate side-chains
  105 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
A 356 ASN
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1170 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 = 0.3504 r_free = 0.3504 target = 0.066540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.049657 restraints weight = 51911.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.050622 restraints weight = 42574.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.051289 restraints weight = 35985.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.5146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6822  Z= 0.254
  Angle     :  0.785   9.058   9226  Z= 0.401
  Chirality :  0.045   0.181   1057
  Planarity :  0.005   0.063   1145
  Dihedral  :  5.203  21.271    905
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 20.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.28), residues: 828
  helix:  0.11 (0.21), residues: 531
  sheet: -2.86 (0.43), residues: 103
  loop : -2.36 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 130 
 HIS   0.006   0.001   HIS A 297 
 PHE   0.020   0.002   PHE A 125 
 TYR   0.013   0.002   TYR A1241 
 ARG   0.011   0.001   ARG A 305 

*********************** 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
  133 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9449 (t80) cc_final: 0.9153 (t80)
REVERT: A  180 THR cc_start: 0.9764 (p) cc_final: 0.9529 (p)
REVERT: A  184 PHE cc_start: 0.9558 (m-10) cc_final: 0.9333 (m-80)
REVERT: A  227 CYS cc_start: 0.9432 (t) cc_final: 0.9192 (t)
REVERT: A  243 TYR cc_start: 0.7694 (p90) cc_final: 0.7292 (m-80)
REVERT: A  297 HIS cc_start: 0.9347 (t-90) cc_final: 0.9053 (t-90)
REVERT: A  508 ASP cc_start: 0.9410 (m-30) cc_final: 0.9167 (t70)
REVERT: A  520 MET cc_start: 0.7787 (ptt) cc_final: 0.7238 (ptt)
REVERT: A  987 PHE cc_start: 0.9522 (m-10) cc_final: 0.8991 (m-80)
REVERT: A 1001 PHE cc_start: 0.8911 (m-10) cc_final: 0.8603 (m-10)
REVERT: A 1016 ASP cc_start: 0.9419 (t0) cc_final: 0.9143 (p0)
REVERT: A 1083 TYR cc_start: 0.9005 (m-80) cc_final: 0.8413 (m-80)
REVERT: A 1188 TRP cc_start: 0.8764 (p90) cc_final: 0.8317 (p90)
REVERT: A 1198 MET cc_start: 0.8843 (mmp) cc_final: 0.8164 (ttm)
REVERT: A 1220 MET cc_start: 0.7676 (mtm) cc_final: 0.7430 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1495
  time to fit residues: 28.6184
Evaluate side-chains
  107 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 76 optimal weight:    7.9990
   chunk 29 optimal weight:   20.0000
   chunk 7 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 75 optimal weight:    0.1980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.068348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.050436 restraints weight = 45523.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.051361 restraints weight = 37198.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.052229 restraints weight = 32004.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.5623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6822  Z= 0.185
  Angle     :  0.754   9.318   9226  Z= 0.379
  Chirality :  0.044   0.180   1057
  Planarity :  0.004   0.060   1145
  Dihedral  :  4.936  21.621    905
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.29), residues: 828
  helix:  0.57 (0.22), residues: 528
  sheet: -2.56 (0.45), residues: 98
  loop : -2.28 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 130 
 HIS   0.005   0.001   HIS A1010 
 PHE   0.029   0.002   PHE A 125 
 TYR   0.018   0.001   TYR A 445 
 ARG   0.012   0.001   ARG A1148 

*********************** 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
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.719 
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  180 THR cc_start: 0.9748 (p) cc_final: 0.9510 (p)
REVERT: A  226 MET cc_start: 0.9417 (mpp) cc_final: 0.9043 (mpp)
REVERT: A  227 CYS cc_start: 0.9321 (t) cc_final: 0.9042 (t)
REVERT: A  243 TYR cc_start: 0.7607 (p90) cc_final: 0.7200 (m-80)
REVERT: A  297 HIS cc_start: 0.9203 (t-90) cc_final: 0.8964 (t-90)
REVERT: A  423 PHE cc_start: 0.9494 (m-10) cc_final: 0.9231 (m-80)
REVERT: A  508 ASP cc_start: 0.9375 (m-30) cc_final: 0.9167 (t70)
REVERT: A  520 MET cc_start: 0.7433 (ptt) cc_final: 0.6889 (ptt)
REVERT: A  987 PHE cc_start: 0.9471 (m-10) cc_final: 0.8889 (m-80)
REVERT: A 1001 PHE cc_start: 0.8856 (m-10) cc_final: 0.8629 (m-10)
REVERT: A 1016 ASP cc_start: 0.9424 (t0) cc_final: 0.9136 (p0)
REVERT: A 1198 MET cc_start: 0.8879 (mmp) cc_final: 0.8189 (ttm)
REVERT: A 1220 MET cc_start: 0.7639 (mtm) cc_final: 0.7296 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1389
  time to fit residues: 28.1606
Evaluate side-chains
  117 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 61 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0050
   chunk 29 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5572

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
A1170 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.110247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.089109 restraints weight = 49137.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.090986 restraints weight = 28242.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.092145 restraints weight = 18472.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.6170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6822  Z= 0.184
  Angle     :  0.767   9.508   9226  Z= 0.386
  Chirality :  0.044   0.184   1057
  Planarity :  0.004   0.049   1145
  Dihedral  :  4.720  21.234    905
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.29), residues: 828
  helix:  0.78 (0.22), residues: 530
  sheet: -2.16 (0.51), residues: 86
  loop : -2.52 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 995 
 HIS   0.005   0.001   HIS A 239 
 PHE   0.055   0.002   PHE A 798 
 TYR   0.013   0.001   TYR A 538 
 ARG   0.008   0.001   ARG A1148 

*********************** 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
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.791 
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  227 CYS cc_start: 0.9316 (t) cc_final: 0.9019 (t)
REVERT: A  243 TYR cc_start: 0.7548 (p90) cc_final: 0.7207 (m-80)
REVERT: A  297 HIS cc_start: 0.9280 (t-90) cc_final: 0.9028 (t-90)
REVERT: A  423 PHE cc_start: 0.9499 (m-10) cc_final: 0.9220 (m-80)
REVERT: A  508 ASP cc_start: 0.9236 (m-30) cc_final: 0.9003 (t70)
REVERT: A  520 MET cc_start: 0.6672 (ptt) cc_final: 0.6189 (ptt)
REVERT: A  545 MET cc_start: 0.8388 (tpt) cc_final: 0.8140 (tpt)
REVERT: A  987 PHE cc_start: 0.9416 (m-10) cc_final: 0.8839 (m-80)
REVERT: A  996 PHE cc_start: 0.8922 (m-80) cc_final: 0.8339 (m-80)
REVERT: A 1001 PHE cc_start: 0.8779 (m-10) cc_final: 0.8553 (m-10)
REVERT: A 1016 ASP cc_start: 0.9370 (t0) cc_final: 0.9032 (p0)
REVERT: A 1198 MET cc_start: 0.8947 (mmp) cc_final: 0.8314 (ttm)
REVERT: A 1215 ARG cc_start: 0.9403 (ptt-90) cc_final: 0.9090 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7214 (mtm) cc_final: 0.6773 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1583
  time to fit residues: 31.6937
Evaluate side-chains
  116 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 72 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0370
   chunk 35 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    1.5862

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
A 239 HIS
A 356 ASN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 883 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.072190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.054566 restraints weight = 51020.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.055661 restraints weight = 41598.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.056504 restraints weight = 35034.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.6201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   6822  Z= 0.213
  Angle     :  0.776   9.466   9226  Z= 0.394
  Chirality :  0.045   0.173   1057
  Planarity :  0.005   0.049   1145
  Dihedral  :  4.800  21.945    905
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.28), residues: 828
  helix:  0.64 (0.22), residues: 530
  sheet: -2.34 (0.45), residues: 101
  loop : -2.40 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.083   0.003   TRP A 130 
 HIS   0.011   0.001   HIS A 292 
 PHE   0.044   0.002   PHE A 798 
 TYR   0.011   0.001   TYR A 538 
 ARG   0.009   0.001   ARG A 305 

********************** 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
  136 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.744 
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: 0.9379 (t80) cc_final: 0.9042 (t80)
REVERT: A  227 CYS cc_start: 0.9298 (t) cc_final: 0.9040 (t)
REVERT: A  243 TYR cc_start: 0.7618 (p90) cc_final: 0.7254 (m-80)
REVERT: A  297 HIS cc_start: 0.9251 (t-90) cc_final: 0.8990 (t-90)
REVERT: A  423 PHE cc_start: 0.9561 (m-10) cc_final: 0.9346 (m-80)
REVERT: A  508 ASP cc_start: 0.9331 (m-30) cc_final: 0.9076 (t70)
REVERT: A  919 MET cc_start: 0.8654 (mmt) cc_final: 0.8429 (mmt)
REVERT: A  987 PHE cc_start: 0.9478 (m-10) cc_final: 0.8900 (m-80)
REVERT: A  996 PHE cc_start: 0.8953 (m-80) cc_final: 0.8314 (m-80)
REVERT: A 1001 PHE cc_start: 0.8814 (m-10) cc_final: 0.8504 (m-10)
REVERT: A 1016 ASP cc_start: 0.9414 (t0) cc_final: 0.9145 (p0)
REVERT: A 1188 TRP cc_start: 0.8781 (p90) cc_final: 0.8157 (p90)
REVERT: A 1198 MET cc_start: 0.8865 (mmp) cc_final: 0.8187 (ttm)
REVERT: A 1220 MET cc_start: 0.7632 (mtm) cc_final: 0.7378 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1354
  time to fit residues: 26.7306
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  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 70 optimal weight:    7.9990
   chunk 47 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 356 ASN
** A 389 GLN ** 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 = 0.3468 r_free = 0.3468 target = 0.065791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.049205 restraints weight = 52824.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.050192 restraints weight = 42776.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.050979 restraints weight = 35928.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.6028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076   6822  Z= 0.355
  Angle     :  0.899   9.619   9226  Z= 0.470
  Chirality :  0.050   0.288   1057
  Planarity :  0.006   0.071   1145
  Dihedral  :  5.569  22.541    905
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 27.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.27), residues: 828
  helix: -0.28 (0.21), residues: 527
  sheet: -2.27 (0.46), residues: 102
  loop : -2.36 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.004   TRP A 130 
 HIS   0.012   0.002   HIS A 288 
 PHE   0.041   0.003   PHE A 798 
 TYR   0.017   0.002   TYR A 243 
 ARG   0.011   0.001   ARG A 305 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2268.77 seconds
wall clock time: 41 minutes 36.70 seconds (2496.70 seconds total)