Starting phenix.real_space_refine
on Wed Sep 17 14:27:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kjc_62366/09_2025/9kjc_62366.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kjc_62366/09_2025/9kjc_62366.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kjc_62366/09_2025/9kjc_62366.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kjc_62366/09_2025/9kjc_62366.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kjc_62366/09_2025/9kjc_62366.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kjc_62366/09_2025/9kjc_62366.map"
  }
  resolution = 3.6
  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=   0.001 sd=   0.053
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      37      5.16       5
     C    5789      2.51       5
     N    1521      2.21       5
     O    1668      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9015
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1168, 8981
          Classifications: {'peptide': 1168}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 29, 'TRANS': 1138}
          Chain breaks: 1
          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: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'BLD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.42, per 1000 atoms: 0.27
  Number of scatterers: 9015
  At special positions: 0
  Unit cell: (78.66, 106.875, 138.51, 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      37     16.00
     O    1668      8.00
     N    1521      7.00
     C    5789      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: 0.91
  Conformation dependent library (CDL) restraints added in 366.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      63.9% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 29
    Processing helix  chain 'A' and resid 34 through 71
      Proline residue:  A  56  - end of helix
    Processing helix  chain 'A' and resid 75 through 130
    Processing helix  chain 'A' and resid 139 through 160
      removed outlier: 3.617A  pdb=" N   PHE A 146 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 184
      removed outlier: 3.539A  pdb=" N   GLY A 180 " --> pdb=" O   GLY A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 233
      removed outlier: 3.794A  pdb=" N   LEU A 190 " --> pdb=" O   LYS A 186 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL A 192 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
      Proline residue:  A 196  - end of helix
      removed outlier: 4.407A  pdb=" N   GLN A 229 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   ALA A 230 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ILE A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 242 through 297
      removed outlier: 3.560A  pdb=" N   ASN A 248 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ALA A 249 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   TYR A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 343
      removed outlier: 4.510A  pdb=" N   ILE A 341 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ILE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ASN A 343 " --> pdb=" O   MET A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 414
    Processing helix  chain 'A' and resid 432 through 434
      No H-bonds generated for 'chain 'A' and resid 432 through 434'
    Processing helix  chain 'A' and resid 439 through 441
      No H-bonds generated for 'chain 'A' and resid 439 through 441'
    Processing helix  chain 'A' and resid 456 through 462
      removed outlier: 3.684A  pdb=" N   ASN A 460 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 479
      removed outlier: 3.910A  pdb=" N   ALA A 479 " --> pdb=" O   ALA A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 487
      removed outlier: 3.607A  pdb=" N   THR A 487 " --> pdb=" O   HIS A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 521
      removed outlier: 3.762A  pdb=" N   ALA A 515 " --> pdb=" O   ARG A 511 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 520 " --> pdb=" O   ARG A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 548
      removed outlier: 4.248A  pdb=" N   VAL A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   GLN A 543 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   GLU A 544 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ALA A 545 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 593
      removed outlier: 4.197A  pdb=" N   SER A 592 " --> pdb=" O   ILE A 589 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLY A 593 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 589 through 593'
    Processing helix  chain 'A' and resid 595 through 605
      removed outlier: 3.742A  pdb=" N   VAL A 605 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 680
    Processing helix  chain 'A' and resid 683 through 715
      removed outlier: 3.791A  pdb=" N   SER A 687 " --> pdb=" O   GLU A 683 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   MET A 689 " --> pdb=" O   PRO A 685 " (cutoff:3.500A)
      Proline residue:  A 702  - end of helix
    Processing helix  chain 'A' and resid 719 through 773
      removed outlier: 3.539A  pdb=" N   MET A 723 " --> pdb=" O   ASP A 719 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU A 724 " --> pdb=" O   TYR A 720 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ARG A 725 " --> pdb=" O   ASP A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 780
      removed outlier: 3.894A  pdb=" N   PHE A 779 " --> pdb=" O   GLU A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 829
      removed outlier: 4.016A  pdb=" N   ALA A 794 " --> pdb=" O   ALA A 790 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR A 795 " --> pdb=" O   ALA A 791 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA A 797 " --> pdb=" O   LEU A 793 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ALA A 798 " --> pdb=" O   ALA A 794 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A 800 " --> pdb=" O   ASP A 796 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   LYS A 801 " --> pdb=" O   ALA A 797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 853
      removed outlier: 3.811A  pdb=" N   LEU A 835 " --> pdb=" O   ARG A 831 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 836 " --> pdb=" O   VAL A 832 " (cutoff:3.500A)
      Proline residue:  A 841  - end of helix
    Processing helix  chain 'A' and resid 854 through 856
      No H-bonds generated for 'chain 'A' and resid 854 through 856'
    Processing helix  chain 'A' and resid 860 through 865
    Processing helix  chain 'A' and resid 865 through 878
      removed outlier: 3.841A  pdb=" N   SER A 869 " --> pdb=" O   HIS A 865 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   MET A 870 " --> pdb=" O   ALA A 866 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN A 878 " --> pdb=" O   GLU A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 884
      removed outlier: 3.952A  pdb=" N   ALA A 884 " --> pdb=" O   ARG A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 941
      removed outlier: 3.778A  pdb=" N   SER A 893 " --> pdb=" O   SER A 889 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 894 " --> pdb=" O   LYS A 890 " (cutoff:3.500A)
      Proline residue:  A 902  - end of helix
    Processing helix  chain 'A' and resid 948 through 968
    Processing helix  chain 'A' and resid 968 through 975
      removed outlier: 4.047A  pdb=" N   GLU A 972 " --> pdb=" O   SER A 968 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 988
      removed outlier: 3.553A  pdb=" N   LEU A 987 " --> pdb=" O   VAL A 983 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP A 988 " --> pdb=" O   PHE A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1050 through 1053
    Processing helix  chain 'A' and resid 1054 through 1059
      removed outlier: 4.405A  pdb=" N   GLU A1059 " --> pdb=" O   ILE A1055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1079
      No H-bonds generated for 'chain 'A' and resid 1077 through 1079'
    Processing helix  chain 'A' and resid 1080 through 1086
      removed outlier: 3.899A  pdb=" N   LEU A1084 " --> pdb=" O   ASN A1080 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1115 through 1123
      removed outlier: 4.361A  pdb=" N   ILE A1119 " --> pdb=" O   GLU A1115 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ASP A1120 " --> pdb=" O   SER A1116 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG A1123 " --> pdb=" O   ILE A1119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1133
      removed outlier: 3.598A  pdb=" N   GLY A1133 " --> pdb=" O   GLY A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1150 through 1166
      removed outlier: 3.955A  pdb=" N   LYS A1154 " --> pdb=" O   SER A1150 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLN A1155 " --> pdb=" O   GLY A1151 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ARG A1156 " --> pdb=" O   GLY A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1185 through 1194
      removed outlier: 3.671A  pdb=" N   GLU A1189 " --> pdb=" O   CYS A1185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1229 through 1235
      removed outlier: 4.462A  pdb=" N   SER A1235 " --> pdb=" O   SER A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1239 through 1252
      removed outlier: 3.724A  pdb=" N   ARG A1243 " --> pdb=" O   GLY A1239 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU A1244 " --> pdb=" O   ALA A1240 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 390
      removed outlier: 4.875A  pdb=" N   VAL A 370 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   SER A 421 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 557 through 558
      removed outlier: 5.517A  pdb=" N   ALA A 397 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE A 574 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   VAL A 399 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   VAL A 573 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 443 through 445
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1031 through 1034
      removed outlier: 5.979A  pdb=" N   PHE A1031 " --> pdb=" O   HIS A1014 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   HIS A1014 " --> pdb=" O   PHE A1031 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU A1033 " --> pdb=" O   PHE A1012 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1041
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1216 through 1220
      removed outlier: 3.603A  pdb=" N   GLY A1228 " --> pdb=" O   ILE A1216 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL A1218 " --> pdb=" O   GLU A1226 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   GLU A1226 " --> pdb=" O   VAL A1218 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLN A1220 " --> pdb=" O   ILE A1224 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ILE A1224 " --> pdb=" O   GLN A1220 " (cutoff:3.500A)

    529 hydrogen bonds defined for protein.
    1563 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: 1.60

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1519
        1.32 -     1.45: 2400
        1.45 -     1.57: 5203
        1.57 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 9187
  Sorted by residual:
  bond pdb=" N   THR A1249 "
       pdb=" CA  THR A1249 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.17e-02 7.31e+03 7.39e+00
  bond pdb=" N   LEU A1245 "
       pdb=" CA  LEU A1245 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.19e-02 7.06e+03 6.85e+00
  bond pdb=" N   ARG A1251 "
       pdb=" CA  ARG A1251 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.17e-02 7.31e+03 6.62e+00
  bond pdb=" N   HIS A1250 "
       pdb=" CA  HIS A1250 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.23e-02 6.61e+03 6.34e+00
  bond pdb=" N   LEU A1244 "
       pdb=" CA  LEU A1244 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.20e-02 6.94e+03 5.96e+00
  ... (remaining 9182 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 12152
        1.90 -     3.80: 234
        3.80 -     5.69: 36
        5.69 -     7.59: 10
        7.59 -     9.49: 8
  Bond angle restraints: 12440
  Sorted by residual:
  angle pdb=" N   ARG A1243 "
        pdb=" CA  ARG A1243 "
        pdb=" C   ARG A1243 "
      ideal   model   delta    sigma   weight residual
     111.11  105.50    5.61 1.20e+00 6.94e-01 2.18e+01
  angle pdb=" N   GLU A 729 "
        pdb=" CA  GLU A 729 "
        pdb=" CB  GLU A 729 "
      ideal   model   delta    sigma   weight residual
     110.39  117.36   -6.97 1.66e+00 3.63e-01 1.76e+01
  angle pdb=" C   LYS A 728 "
        pdb=" N   GLU A 729 "
        pdb=" CA  GLU A 729 "
      ideal   model   delta    sigma   weight residual
     120.72  113.78    6.94 1.67e+00 3.59e-01 1.73e+01
  angle pdb=" C   SER A 183 "
        pdb=" N   ALA A 184 "
        pdb=" CA  ALA A 184 "
      ideal   model   delta    sigma   weight residual
     121.54  114.20    7.34 1.91e+00 2.74e-01 1.48e+01
  angle pdb=" C   GLY A 977 "
        pdb=" N   GLU A 978 "
        pdb=" CA  GLU A 978 "
      ideal   model   delta    sigma   weight residual
     121.31  126.88   -5.57 1.49e+00 4.50e-01 1.40e+01
  ... (remaining 12435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.44: 5255
       26.44 -    52.87: 220
       52.87 -    79.31: 25
       79.31 -   105.75: 9
      105.75 -   132.18: 1
  Dihedral angle restraints: 5510
    sinusoidal: 2165
      harmonic: 3345
  Sorted by residual:
  dihedral pdb=" CA  GLU A 978 "
           pdb=" C   GLU A 978 "
           pdb=" N   ALA A 979 "
           pdb=" CA  ALA A 979 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.98  -43.02     0      5.00e+00 4.00e-02 7.40e+01
  dihedral pdb=" CA  TRP A 185 "
           pdb=" C   TRP A 185 "
           pdb=" N   LYS A 186 "
           pdb=" CA  LYS A 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.73   30.27     0      5.00e+00 4.00e-02 3.67e+01
  dihedral pdb=" C06 BLD A1301 "
           pdb=" C07 BLD A1301 "
           pdb=" O07 BLD A1301 "
           pdb=" C08 BLD A1301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.68   64.50 -132.18     1      3.00e+01 1.11e-03 1.78e+01
  ... (remaining 5507 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1123
       0.048 -    0.097: 254
       0.097 -    0.145: 54
       0.145 -    0.193: 4
       0.193 -    0.241: 3
  Chirality restraints: 1438
  Sorted by residual:
  chirality pdb=" C10 BLD A1301 "
            pdb=" C01 BLD A1301 "
            pdb=" C05 BLD A1301 "
            pdb=" C09 BLD A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -3.02   -2.78   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" C09 BLD A1301 "
            pdb=" C08 BLD A1301 "
            pdb=" C10 BLD A1301 "
            pdb=" C11 BLD A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.64    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  LEU A1247 "
            pdb=" N   LEU A1247 "
            pdb=" C   LEU A1247 "
            pdb=" CB  LEU A1247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1435 not shown)

  Planarity restraints: 1579
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1243 "    0.530 9.50e-02 1.11e+02   2.38e-01 3.46e+01
        pdb=" NE  ARG A1243 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1243 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1243 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1243 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1251 "   -0.365 9.50e-02 1.11e+02   1.64e-01 1.64e+01
        pdb=" NE  ARG A1251 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1251 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1251 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1251 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 701 "   -0.046 5.00e-02 4.00e+02   7.09e-02 8.03e+00
        pdb=" N   PRO A 702 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 702 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 702 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1576 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 961
        2.74 -     3.28: 9510
        3.28 -     3.82: 14576
        3.82 -     4.36: 16271
        4.36 -     4.90: 27699
  Nonbonded interactions: 69017
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 395 "
            pdb=" OD1 ASP A 569 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" CZ  PHE A 305 "
            pdb=" C26 BLD A1301 "
     model   vdw
     2.246 3.760
  nonbonded pdb=" O   GLY A1152 "
            pdb=" NE2 GLN A1155 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   ALA A 475 "
            pdb=" OG  SER A 478 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   PRO A 522 "
            pdb=" NH1 ARG A 553 "
     model   vdw
     2.288 3.120
  ... (remaining 69012 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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.090
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9187  Z= 0.188
  Angle     :  0.682   9.488  12440  Z= 0.387
  Chirality :  0.043   0.241   1438
  Planarity :  0.008   0.238   1579
  Dihedral  : 14.664 132.183   3374
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  0.42 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.25), residues: 1164
  helix:  1.38 (0.20), residues: 688
  sheet: -1.18 (0.61), residues: 78
  loop : -2.62 (0.28), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1060 
 TYR   0.014   0.001   TYR A 220 
 PHE   0.017   0.001   PHE A  69 
 TRP   0.009   0.001   TRP A 108 
 HIS   0.008   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9187)
  covalent geometry    : angle       0.68186 (12440)
  hydrogen bonds       : bond        0.17519 (  529)
  hydrogen bonds       : angle       5.90402 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  381 MET cc_start: 0.4896 (mmm) cc_final: 0.4634 (tmm)
REVERT: A  526 LEU cc_start: 0.8801 (mm) cc_final: 0.8577 (mm)
REVERT: A  755 MET cc_start: 0.6994 (ttp) cc_final: 0.6756 (ttt)
  outliers start: 6
  outliers final: 1
  residues processed: 106
  average time/residue: 0.0776
  time to fit residues: 12.3352
Evaluate side-chains
  87 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1245 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   30.0000
   chunk 100 optimal weight:    7.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  51 HIS
A 168 HIS
A 298 GLN
A 360 GLN
A 362 HIS
A 481 ASN
A 850 GLN
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 ASN
A 921 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.202636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.125503 restraints weight = 13697.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.129976 restraints weight = 8068.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.129878 restraints weight = 5077.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.130087 restraints weight = 5147.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.130346 restraints weight = 4849.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   9187  Z= 0.315
  Angle     :  0.743  10.134  12440  Z= 0.400
  Chirality :  0.046   0.176   1438
  Planarity :  0.005   0.076   1579
  Dihedral  :  5.711  49.908   1355
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.25 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.73 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.24), residues: 1164
  helix:  0.80 (0.19), residues: 709
  sheet: -1.47 (0.56), residues: 81
  loop : -2.81 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1123 
 TYR   0.017   0.002   TYR A 740 
 PHE   0.023   0.002   PHE A1061 
 TRP   0.017   0.002   TRP A 684 
 HIS   0.016   0.002   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00730 ( 9187)
  covalent geometry    : angle       0.74288 (12440)
  hydrogen bonds       : bond        0.09471 (  529)
  hydrogen bonds       : angle       5.44300 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 ILE cc_start: 0.6446 (mt) cc_final: 0.6219 (mt)
REVERT: A  526 LEU cc_start: 0.8940 (mm) cc_final: 0.8592 (mm)
REVERT: A  729 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7829 (pm20)
REVERT: A  755 MET cc_start: 0.7150 (ttp) cc_final: 0.6919 (ttt)
  outliers start: 15
  outliers final: 8
  residues processed: 111
  average time/residue: 0.0813
  time to fit residues: 13.3476
Evaluate side-chains
  95 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1106 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 89 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 105 optimal weight:    7.9990
   chunk 69 optimal weight:    0.0170
   chunk 39 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 57 optimal weight:   40.0000
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.3622

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

Flipped N/Q/H residues before XYZ refinement:
A 460 ASN
A 878 ASN
** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 GLN ** 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 = 0.4476 r_free = 0.4476 target = 0.206719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.141709 restraints weight = 13615.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.137344 restraints weight = 8917.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139989 restraints weight = 6336.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.139187 restraints weight = 4567.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.139414 restraints weight = 4673.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9187  Z= 0.168
  Angle     :  0.593   9.450  12440  Z= 0.318
  Chirality :  0.041   0.175   1438
  Planarity :  0.004   0.077   1579
  Dihedral  :  5.246  40.654   1353
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.25 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.25), residues: 1164
  helix:  1.38 (0.20), residues: 697
  sheet: -1.30 (0.58), residues: 76
  loop : -2.70 (0.27), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1123 
 TYR   0.016   0.001   TYR A 220 
 PHE   0.015   0.001   PHE A  69 
 TRP   0.014   0.001   TRP A 684 
 HIS   0.002   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9187)
  covalent geometry    : angle       0.59279 (12440)
  hydrogen bonds       : bond        0.07708 (  529)
  hydrogen bonds       : angle       4.81217 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 ILE cc_start: 0.6308 (mt) cc_final: 0.6067 (mt)
REVERT: A  526 LEU cc_start: 0.8894 (mm) cc_final: 0.8613 (mm)
REVERT: A  729 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7814 (pm20)
REVERT: A  755 MET cc_start: 0.7018 (ttp) cc_final: 0.6783 (ttt)
REVERT: A  819 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7647 (mm)
  outliers start: 23
  outliers final: 13
  residues processed: 112
  average time/residue: 0.0842
  time to fit residues: 14.0115
Evaluate side-chains
  101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  796 ASP
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  991 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 17 optimal weight:    0.7980
   chunk 113 optimal weight:   40.0000
   chunk 24 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 111 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 460 ASN
A 878 ASN
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1105 ASN
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.204753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.130738 restraints weight = 13842.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.132667 restraints weight = 8591.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.133451 restraints weight = 5965.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133794 restraints weight = 5312.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.133994 restraints weight = 5211.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9187  Z= 0.190
  Angle     :  0.620   9.279  12440  Z= 0.330
  Chirality :  0.042   0.160   1438
  Planarity :  0.004   0.076   1579
  Dihedral  :  5.308  36.565   1353
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.19 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.25), residues: 1164
  helix:  1.33 (0.20), residues: 699
  sheet: -1.46 (0.57), residues: 75
  loop : -2.87 (0.27), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1123 
 TYR   0.015   0.001   TYR A 220 
 PHE   0.020   0.002   PHE A  69 
 TRP   0.012   0.001   TRP A 684 
 HIS   0.003   0.001   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 9187)
  covalent geometry    : angle       0.62040 (12440)
  hydrogen bonds       : bond        0.08001 (  529)
  hydrogen bonds       : angle       4.83114 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7717 (tm-30)
REVERT: A  226 ILE cc_start: 0.6383 (mt) cc_final: 0.6171 (mt)
REVERT: A  526 LEU cc_start: 0.8875 (mm) cc_final: 0.8534 (mm)
REVERT: A  729 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7775 (pm20)
REVERT: A  755 MET cc_start: 0.7068 (ttp) cc_final: 0.6847 (ttt)
REVERT: A  819 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7682 (mm)
  outliers start: 26
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0771
  time to fit residues: 12.9505
Evaluate side-chains
  107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  604 MET
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  796 ASP
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1106 ILE
Chi-restraints excluded: chain A residue 1164 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 83 optimal weight:    0.8980
   chunk 34 optimal weight:   30.0000
   chunk 93 optimal weight:    5.9990
   chunk 7 optimal weight:    0.5980
   chunk 110 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 101 optimal weight:    0.0870
   chunk 91 optimal weight:    0.0010
   chunk 51 optimal weight:   20.0000
   overall best weight:    0.4964

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

Flipped N/Q/H residues before XYZ refinement:
A 878 ASN
A 903 GLN
** A1155 GLN ** 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 = 0.4516 r_free = 0.4516 target = 0.210475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.148016 restraints weight = 13832.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.143126 restraints weight = 9332.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.145996 restraints weight = 6493.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.145517 restraints weight = 4796.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.145637 restraints weight = 4737.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9187  Z= 0.127
  Angle     :  0.561   9.349  12440  Z= 0.293
  Chirality :  0.040   0.182   1438
  Planarity :  0.004   0.072   1579
  Dihedral  :  5.072  35.470   1353
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.77 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.25), residues: 1164
  helix:  1.86 (0.20), residues: 687
  sheet: -1.23 (0.55), residues: 81
  loop : -2.74 (0.27), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 553 
 TYR   0.019   0.001   TYR A 220 
 PHE   0.024   0.001   PHE A 438 
 TRP   0.010   0.001   TRP A 684 
 HIS   0.002   0.000   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9187)
  covalent geometry    : angle       0.56063 (12440)
  hydrogen bonds       : bond        0.06275 (  529)
  hydrogen bonds       : angle       4.32380 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8136 (m-10) cc_final: 0.7849 (m-10)
REVERT: A  130 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7826 (tm-30)
REVERT: A  226 ILE cc_start: 0.6167 (mt) cc_final: 0.5942 (mt)
REVERT: A  381 MET cc_start: 0.4924 (mmm) cc_final: 0.4565 (tmm)
REVERT: A  526 LEU cc_start: 0.8817 (mm) cc_final: 0.8479 (mm)
REVERT: A  729 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7742 (pm20)
REVERT: A  755 MET cc_start: 0.6946 (ttp) cc_final: 0.6687 (ttt)
REVERT: A  878 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7321 (p0)
  outliers start: 19
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0767
  time to fit residues: 12.9053
Evaluate side-chains
  101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  878 ASN
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  969 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0770
   chunk 19 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
A 878 ASN
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.209842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.147893 restraints weight = 13822.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.145856 restraints weight = 10373.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.146851 restraints weight = 7318.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.147356 restraints weight = 5953.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.147518 restraints weight = 5673.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9187  Z= 0.127
  Angle     :  0.562   9.041  12440  Z= 0.294
  Chirality :  0.040   0.246   1438
  Planarity :  0.004   0.070   1579
  Dihedral  :  5.035  36.188   1353
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.61 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.25), residues: 1164
  helix:  1.93 (0.20), residues: 692
  sheet: -1.14 (0.56), residues: 81
  loop : -2.76 (0.27), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1029 
 TYR   0.017   0.001   TYR A 220 
 PHE   0.016   0.001   PHE A 372 
 TRP   0.010   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9187)
  covalent geometry    : angle       0.56202 (12440)
  hydrogen bonds       : bond        0.06199 (  529)
  hydrogen bonds       : angle       4.28130 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8006 (m-10) cc_final: 0.7716 (m-10)
REVERT: A  130 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7815 (tm-30)
REVERT: A  381 MET cc_start: 0.5067 (mmm) cc_final: 0.4632 (tmm)
REVERT: A  526 LEU cc_start: 0.8819 (mm) cc_final: 0.8481 (mm)
REVERT: A  729 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7749 (pm20)
REVERT: A  755 MET cc_start: 0.6968 (ttp) cc_final: 0.6711 (ttt)
REVERT: A  819 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7613 (mt)
REVERT: A 1029 ARG cc_start: 0.7751 (ptm-80) cc_final: 0.7524 (tmm160)
  outliers start: 20
  outliers final: 13
  residues processed: 107
  average time/residue: 0.0801
  time to fit residues: 12.8701
Evaluate side-chains
  105 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1164 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0470
   chunk 62 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 99 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   overall best weight:    1.6882

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

Flipped N/Q/H residues before XYZ refinement:
A 602 GLN
A 878 ASN
** A1155 GLN ** 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 = 0.4467 r_free = 0.4467 target = 0.205480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.129595 restraints weight = 13826.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133452 restraints weight = 7240.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.135840 restraints weight = 5009.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.136959 restraints weight = 4138.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.137601 restraints weight = 3747.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9187  Z= 0.181
  Angle     :  0.611  10.619  12440  Z= 0.323
  Chirality :  0.042   0.189   1438
  Planarity :  0.004   0.071   1579
  Dihedral  :  5.205  34.983   1353
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.51 %
    Favored  : 79.18 %
  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 aren not related in a simple way.
  whole:  0.03 (0.25), residues: 1164
  helix:  1.60 (0.20), residues: 698
  sheet: -1.08 (0.57), residues: 80
  loop : -2.84 (0.27), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 553 
 TYR   0.015   0.001   TYR A 220 
 PHE   0.015   0.001   PHE A 309 
 TRP   0.009   0.001   TRP A 684 
 HIS   0.003   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 9187)
  covalent geometry    : angle       0.61097 (12440)
  hydrogen bonds       : bond        0.07539 (  529)
  hydrogen bonds       : angle       4.61682 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7615 (tm-30)
REVERT: A  226 ILE cc_start: 0.6300 (mt) cc_final: 0.6062 (mt)
REVERT: A  526 LEU cc_start: 0.8756 (mm) cc_final: 0.8341 (mm)
REVERT: A  729 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7757 (pm20)
REVERT: A  755 MET cc_start: 0.7000 (ttp) cc_final: 0.6763 (ttt)
REVERT: A  815 MET cc_start: 0.7529 (tpp) cc_final: 0.7023 (tpp)
REVERT: A  819 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7614 (mm)
  outliers start: 22
  outliers final: 15
  residues processed: 108
  average time/residue: 0.0791
  time to fit residues: 12.9925
Evaluate side-chains
  107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1164 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 113 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 76 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 105 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 106 optimal weight:   20.0000
   chunk 4 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 886 ASN
A1014 HIS
A1032 ASN
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1205 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.200441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.122980 restraints weight = 13819.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.127260 restraints weight = 7847.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.128037 restraints weight = 5064.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.127874 restraints weight = 4566.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.128218 restraints weight = 4813.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   9187  Z= 0.281
  Angle     :  0.715   9.446  12440  Z= 0.380
  Chirality :  0.045   0.214   1438
  Planarity :  0.004   0.073   1579
  Dihedral  :  5.567  36.540   1353
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.25 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 19.14 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.24), residues: 1164
  helix:  1.13 (0.20), residues: 691
  sheet: -1.07 (0.57), residues: 80
  loop : -2.86 (0.27), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A1161 
 TYR   0.014   0.002   TYR A 220 
 PHE   0.021   0.002   PHE A 309 
 TRP   0.013   0.002   TRP A 684 
 HIS   0.005   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00650 ( 9187)
  covalent geometry    : angle       0.71519 (12440)
  hydrogen bonds       : bond        0.09355 (  529)
  hydrogen bonds       : angle       5.17611 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  130 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7697 (tm-30)
REVERT: A  226 ILE cc_start: 0.6599 (mt) cc_final: 0.6374 (mt)
REVERT: A  381 MET cc_start: 0.4830 (mmm) cc_final: 0.4520 (tmm)
REVERT: A  526 LEU cc_start: 0.8945 (mm) cc_final: 0.8554 (mm)
REVERT: A  729 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7697 (pm20)
REVERT: A  815 MET cc_start: 0.7544 (tpp) cc_final: 0.7119 (tpp)
REVERT: A  819 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7754 (mm)
REVERT: A 1098 PHE cc_start: 0.6430 (m-80) cc_final: 0.6139 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 109
  average time/residue: 0.0734
  time to fit residues: 12.4167
Evaluate side-chains
  105 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  796 ASP
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1106 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 99 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 57 optimal weight:   30.0000
   chunk 114 optimal weight:    5.9990
   chunk 3 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 680 ASN
A 886 ASN
A1032 ASN
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.206421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.135906 restraints weight = 13791.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.137801 restraints weight = 9509.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.136934 restraints weight = 6670.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.137629 restraints weight = 6016.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.137834 restraints weight = 5709.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9187  Z= 0.150
  Angle     :  0.616  10.058  12440  Z= 0.320
  Chirality :  0.041   0.178   1438
  Planarity :  0.004   0.074   1579
  Dihedral  :  5.239  36.867   1353
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 20.40 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.25), residues: 1164
  helix:  1.67 (0.20), residues: 690
  sheet: -0.97 (0.58), residues: 80
  loop : -2.85 (0.27), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1085 
 TYR   0.018   0.001   TYR A 220 
 PHE   0.015   0.001   PHE A 134 
 TRP   0.014   0.001   TRP A 108 
 HIS   0.002   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9187)
  covalent geometry    : angle       0.61554 (12440)
  hydrogen bonds       : bond        0.07237 (  529)
  hydrogen bonds       : angle       4.53580 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7542 (tpp) cc_final: 0.7258 (tpp)
REVERT: A   92 TYR cc_start: 0.8142 (m-10) cc_final: 0.7840 (m-10)
REVERT: A  130 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7825 (tm-30)
REVERT: A  226 ILE cc_start: 0.6435 (mt) cc_final: 0.6176 (mt)
REVERT: A  381 MET cc_start: 0.4892 (mmm) cc_final: 0.4576 (tmm)
REVERT: A  526 LEU cc_start: 0.8905 (mm) cc_final: 0.8507 (mm)
REVERT: A  729 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7740 (pm20)
REVERT: A  819 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7761 (mt)
REVERT: A 1026 MET cc_start: 0.6942 (mmm) cc_final: 0.6599 (mpp)
  outliers start: 17
  outliers final: 14
  residues processed: 114
  average time/residue: 0.0782
  time to fit residues: 13.5404
Evaluate side-chains
  109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue  991 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 92 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 114 optimal weight:    0.2980
   chunk 104 optimal weight:   20.0000
   chunk 95 optimal weight:   10.0000
   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 680 ASN
A 903 GLN
** A1155 GLN ** 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 = 0.4491 r_free = 0.4491 target = 0.207941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.133876 restraints weight = 13650.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.137922 restraints weight = 7004.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 71)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.140456 restraints weight = 4811.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.141618 restraints weight = 3953.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.142390 restraints weight = 3582.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9187  Z= 0.141
  Angle     :  0.622   9.816  12440  Z= 0.321
  Chirality :  0.041   0.172   1438
  Planarity :  0.004   0.072   1579
  Dihedral  :  5.180  37.459   1353
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 21.14 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.25), residues: 1164
  helix:  1.82 (0.20), residues: 690
  sheet: -0.91 (0.57), residues: 81
  loop : -2.83 (0.27), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1029 
 TYR   0.017   0.001   TYR A 220 
 PHE   0.019   0.001   PHE A 438 
 TRP   0.012   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9187)
  covalent geometry    : angle       0.62172 (12440)
  hydrogen bonds       : bond        0.06735 (  529)
  hydrogen bonds       : angle       4.45103 ( 1563)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8163 (m-10) cc_final: 0.7913 (m-10)
REVERT: A  130 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7771 (tm-30)
REVERT: A  226 ILE cc_start: 0.6311 (mt) cc_final: 0.6067 (mt)
REVERT: A  381 MET cc_start: 0.5005 (mmm) cc_final: 0.4695 (tmm)
REVERT: A  526 LEU cc_start: 0.8899 (mm) cc_final: 0.8502 (mm)
REVERT: A  729 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7693 (pm20)
REVERT: A  819 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7584 (mt)
REVERT: A 1026 MET cc_start: 0.6872 (mmm) cc_final: 0.6538 (mpp)
  outliers start: 17
  outliers final: 14
  residues processed: 105
  average time/residue: 0.0779
  time to fit residues: 12.4201
Evaluate side-chains
  106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue  991 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 113 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 91 optimal weight:    0.2980
   chunk 101 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 360 GLN
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.200804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.125284 restraints weight = 13671.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.129445 restraints weight = 8334.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.129573 restraints weight = 5361.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.129867 restraints weight = 5182.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.130065 restraints weight = 4941.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   9187  Z= 0.262
  Angle     :  0.718   9.418  12440  Z= 0.379
  Chirality :  0.045   0.225   1438
  Planarity :  0.004   0.071   1579
  Dihedral  :  5.489  36.362   1353
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.51 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 21.35 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.25), residues: 1164
  helix:  1.27 (0.20), residues: 691
  sheet: -0.97 (0.57), residues: 81
  loop : -2.76 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1161 
 TYR   0.014   0.002   TYR A 220 
 PHE   0.021   0.002   PHE A  69 
 TRP   0.012   0.001   TRP A 684 
 HIS   0.005   0.001   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 ( 9187)
  covalent geometry    : angle       0.71778 (12440)
  hydrogen bonds       : bond        0.08811 (  529)
  hydrogen bonds       : angle       5.04167 ( 1563)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1806.90 seconds
wall clock time: 31 minutes 53.55 seconds (1913.55 seconds total)