Starting phenix.real_space_refine
on Thu Mar 13 18:21:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xmp_22260/03_2025/6xmp_22260_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xmp_22260/03_2025/6xmp_22260.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xmp_22260/03_2025/6xmp_22260.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xmp_22260/03_2025/6xmp_22260.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xmp_22260/03_2025/6xmp_22260_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xmp_22260/03_2025/6xmp_22260_trim.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.060
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    5576      2.51       5
     N    1373      2.21       5
     O    1559      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8545
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1086, 8367
          Classifications: {'peptide': 1086}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 48, 'TRANS': 1037}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 198
          Unresolved non-hydrogen dihedrals: 133
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 113
    Chain: "A"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 178
          Unusual residues: {'LMT': 12}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 264
          Unresolved non-hydrogen angles: 396
          Unresolved non-hydrogen dihedrals: 562
          Unresolved non-hydrogen chiralities: 110
  Time building chain proxies: 5.60, per 1000 atoms: 0.66
  Number of scatterers: 8545
  At special positions: 0
  Unit cell: (83.22, 95.76, 137.94, 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    1559      8.00
     N    1373      7.00
     C    5576      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2042

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 10 sheets defined
      48.2% alpha, 13.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 31
      No H-bonds generated for 'chain 'A' and resid 29 through 31'
    Processing helix  chain 'A' and resid 32 through 44
    Processing helix  chain 'A' and resid 57 through 78
      removed outlier: 3.570A  pdb=" N   LEU A  61 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      Proline residue:  A  75  - end of helix
      removed outlier: 3.801A  pdb=" N   ASN A  78 " --> pdb=" O   MET A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 86
    Processing helix  chain 'A' and resid 149 through 154
      removed outlier: 3.882A  pdb=" N   GLU A 153 " --> pdb=" O   PHE A 149 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   SER A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 149 through 154'
    Processing helix  chain 'A' and resid 156 through 163
      removed outlier: 3.605A  pdb=" N   PHE A 160 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLN A 161 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 188 through 199
      removed outlier: 3.586A  pdb=" N   GLU A 195 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   VAL A 198 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA A 199 " --> pdb=" O   GLU A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 215
    Processing helix  chain 'A' and resid 218 through 246
      removed outlier: 3.509A  pdb=" N   ALA A 242 " --> pdb=" O   GLN A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 250
    Processing helix  chain 'A' and resid 332 through 336
      removed outlier: 4.428A  pdb=" N   ILE A 336 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 375
      removed outlier: 3.938A  pdb=" N   GLU A 375 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 372 through 375'
    Processing helix  chain 'A' and resid 376 through 387
    Processing helix  chain 'A' and resid 396 through 424
      removed outlier: 3.890A  pdb=" N   LEU A 400 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 443
      removed outlier: 4.524A  pdb=" N   LEU A 433 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ASP A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL A 443 " --> pdb=" O   ILE A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 464
      removed outlier: 3.735A  pdb=" N   MET A 453 " --> pdb=" O   MET A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 473
      No H-bonds generated for 'chain 'A' and resid 471 through 473'
    Processing helix  chain 'A' and resid 474 through 480
      removed outlier: 4.451A  pdb=" N   ARG A 480 " --> pdb=" O   PRO A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 3.551A  pdb=" N   ILE A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 606 through 612
      removed outlier: 4.097A  pdb=" N   GLU A 612 " --> pdb=" O   GLU A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 631
      removed outlier: 4.331A  pdb=" N   SER A 631 " --> pdb=" O   SER A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 660
      removed outlier: 4.333A  pdb=" N   VAL A 659 " --> pdb=" O   ASN A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 689
      removed outlier: 3.500A  pdb=" N   THR A 682 " --> pdb=" O   ASP A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 712
    Processing helix  chain 'A' and resid 753 through 758
    Processing helix  chain 'A' and resid 767 through 773
    Processing helix  chain 'A' and resid 778 through 783
    Processing helix  chain 'A' and resid 795 through 807
      removed outlier: 3.690A  pdb=" N   PHE A 799 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 825
      removed outlier: 4.050A  pdb=" N   LEU A 824 " --> pdb=" O   ASP A 820 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LYS A 825 " --> pdb=" O   VAL A 821 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 820 through 825'
    Processing helix  chain 'A' and resid 837 through 852
    Processing helix  chain 'A' and resid 972 through 1012
      removed outlier: 4.466A  pdb=" N   ALA A1012 " --> pdb=" O   ILE A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1018 through 1036
      removed outlier: 3.992A  pdb=" N   CYS A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER A1034 " --> pdb=" O   VAL A1030 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   SER A1036 " --> pdb=" O   PHE A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1055 through 1084
    Processing helix  chain 'A' and resid 1099 through 1120
      removed outlier: 3.740A  pdb=" N   VAL A1114 " --> pdb=" O   LEU A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1152
      removed outlier: 3.691A  pdb=" N   TYR A1137 " --> pdb=" O   ASN A1133 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A1139 " --> pdb=" O   GLY A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1162
    Processing helix  chain 'A' and resid 1168 through 1198
      removed outlier: 4.050A  pdb=" N   ILE A1173 " --> pdb=" O   ASP A1169 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS A1174 " --> pdb=" O   ASP A1170 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE A1184 " --> pdb=" O   LEU A1180 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8
      removed outlier: 3.800A  pdb=" N   VAL A 143 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   HIS A 138 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90
      removed outlier: 4.000A  pdb=" N   LEU A  17 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   TYR A 102 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   SER A  15 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   LEU A 100 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   LEU A  17 " --> pdb=" O   HIS A  98 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   HIS A  98 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY A 111 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 120
      removed outlier: 4.078A  pdb=" N   VAL A 118 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130
    Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 267
      removed outlier: 4.700A  pdb=" N   ASN A 257 " --> pdb=" O   SER A 279 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   LEU A 277 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   LEU A 366 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   ASP A 292 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 303
      removed outlier: 6.836A  pdb=" N   SER A 299 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   VAL A 348 " --> pdb=" O   SER A 299 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ILE A 301 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS A 344 " --> pdb=" O   ASN A 303 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 469
      removed outlier: 6.447A  pdb=" N   GLY A 830 " --> pdb=" O   PHE A 964 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   SER A 966 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ALA A 832 " --> pdb=" O   SER A 966 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   THR A 811 " --> pdb=" O   VAL A 829 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   ILE A 831 " --> pdb=" O   THR A 811 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   MET A 813 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   LEU A 833 " --> pdb=" O   MET A 813 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   GLY A 815 " --> pdb=" O   LEU A 833 " (cutoff:3.500A)
      removed outlier: 9.019A  pdb=" N   TYR A 789 " --> pdb=" O   SER A 693 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   MET A 695 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LEU A 719 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   THR A 766 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   LEU A 721 " --> pdb=" O   THR A 766 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASP A 722 " --> pdb=" O   LEU A 733 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 515 through 516
      removed outlier: 3.799A  pdb=" N   VAL A 498 " --> pdb=" O   HIS A 672 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ILE A 670 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   LEU A 502 " --> pdb=" O   PHE A 668 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   PHE A 668 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   PHE A 665 " --> pdb=" O   SER A 640 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   SER A 640 " --> pdb=" O   PHE A 665 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLY A 667 " --> pdb=" O   LEU A 638 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A 600 " --> pdb=" O   ALA A 593 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA A 593 " --> pdb=" O   PHE A 600 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG A 578 " --> pdb=" O   ILE A 592 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   SER A 594 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   ILE A 576 " --> pdb=" O   SER A 594 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 536 through 537
      removed outlier: 3.779A  pdb=" N   VAL A 536 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1048 through 1049
      removed outlier: 4.931A  pdb=" N   ARG A1048 " --> pdb=" O   ASP A1200 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP A1200 " --> pdb=" O   ARG A1048 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    405 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.30

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2661
        1.34 -     1.46: 1287
        1.46 -     1.57: 4706
        1.57 -     1.69: 0
        1.69 -     1.80: 62
  Bond restraints: 8716
  Sorted by residual:
  bond pdb=" C7  LMT A2003 "
       pdb=" C8  LMT A2003 "
    ideal  model  delta    sigma   weight residual
    1.529  1.440  0.089 2.00e-02 2.50e+03 1.97e+01
  bond pdb=" C5  LMT A2003 "
       pdb=" C6  LMT A2003 "
    ideal  model  delta    sigma   weight residual
    1.527  1.438  0.089 2.00e-02 2.50e+03 1.96e+01
  bond pdb=" C7  LMT A2011 "
       pdb=" C8  LMT A2011 "
    ideal  model  delta    sigma   weight residual
    1.529  1.450  0.079 2.00e-02 2.50e+03 1.56e+01
  bond pdb=" C6  LMT A2003 "
       pdb=" C7  LMT A2003 "
    ideal  model  delta    sigma   weight residual
    1.527  1.448  0.079 2.00e-02 2.50e+03 1.56e+01
  bond pdb=" C7  LMT A2001 "
       pdb=" C8  LMT A2001 "
    ideal  model  delta    sigma   weight residual
    1.529  1.456  0.073 2.00e-02 2.50e+03 1.34e+01
  ... (remaining 8711 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 11581
        2.39 -     4.78: 129
        4.78 -     7.17: 33
        7.17 -     9.56: 23
        9.56 -    11.95: 8
  Bond angle restraints: 11774
  Sorted by residual:
  angle pdb=" C6  LMT A2003 "
        pdb=" C7  LMT A2003 "
        pdb=" C8  LMT A2003 "
      ideal   model   delta    sigma   weight residual
     117.26  105.31   11.95 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" C2  LMT A2003 "
        pdb=" C3  LMT A2003 "
        pdb=" C4  LMT A2003 "
      ideal   model   delta    sigma   weight residual
     117.09  105.72   11.37 3.00e+00 1.11e-01 1.44e+01
  angle pdb=" C2  LMT A2004 "
        pdb=" C3  LMT A2004 "
        pdb=" C4  LMT A2004 "
      ideal   model   delta    sigma   weight residual
     117.09  106.25   10.84 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" C10 LMT A2011 "
        pdb=" C9  LMT A2011 "
        pdb=" C8  LMT A2011 "
      ideal   model   delta    sigma   weight residual
     116.03  105.60   10.43 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" C6  LMT A2008 "
        pdb=" C7  LMT A2008 "
        pdb=" C8  LMT A2008 "
      ideal   model   delta    sigma   weight residual
     117.26  107.07   10.19 3.00e+00 1.11e-01 1.15e+01
  ... (remaining 11769 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 4759
       17.11 -    34.22: 430
       34.22 -    51.33: 69
       51.33 -    68.44: 15
       68.44 -    85.55: 5
  Dihedral angle restraints: 5278
    sinusoidal: 2124
      harmonic: 3154
  Sorted by residual:
  dihedral pdb=" CA  ARG A 760 "
           pdb=" C   ARG A 760 "
           pdb=" N   TYR A 761 "
           pdb=" CA  TYR A 761 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.02  -18.98     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  ASP A 496 "
           pdb=" CB  ASP A 496 "
           pdb=" CG  ASP A 496 "
           pdb=" OD1 ASP A 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.30   58.30     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CB  GLU A 420 "
           pdb=" CG  GLU A 420 "
           pdb=" CD  GLU A 420 "
           pdb=" OE1 GLU A 420 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.55   85.55     1      3.00e+01 1.11e-03 9.84e+00
  ... (remaining 5275 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1090
       0.048 -    0.095: 215
       0.095 -    0.143: 56
       0.143 -    0.191: 5
       0.191 -    0.238: 2
  Chirality restraints: 1368
  Sorted by residual:
  chirality pdb=" C5' LMT A2011 "
            pdb=" C4' LMT A2011 "
            pdb=" C6' LMT A2011 "
            pdb=" O5' LMT A2011 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.27   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" C5' LMT A2008 "
            pdb=" C4' LMT A2008 "
            pdb=" C6' LMT A2008 "
            pdb=" O5' LMT A2008 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.29   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" C4' LMT A2008 "
            pdb=" C3' LMT A2008 "
            pdb=" C5' LMT A2008 "
            pdb=" O1B LMT A2008 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.73    0.18 2.00e-01 2.50e+01 8.02e-01
  ... (remaining 1365 not shown)

  Planarity restraints: 1467
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A1169 "   -0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" CG  ASP A1169 "    0.056 2.00e-02 2.50e+03
        pdb=" OD1 ASP A1169 "   -0.020 2.00e-02 2.50e+03
        pdb=" OD2 ASP A1169 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A1093 "   -0.015 2.00e-02 2.50e+03   3.10e-02 9.60e+00
        pdb=" CD  GLU A1093 "    0.054 2.00e-02 2.50e+03
        pdb=" OE1 GLU A1093 "   -0.020 2.00e-02 2.50e+03
        pdb=" OE2 GLU A1093 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  95 "    0.015 2.00e-02 2.50e+03   3.08e-02 9.50e+00
        pdb=" CD  GLU A  95 "   -0.053 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  95 "    0.019 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  95 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1464 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 626
        2.73 -     3.28: 8334
        3.28 -     3.82: 12849
        3.82 -     4.36: 14042
        4.36 -     4.90: 26133
  Nonbonded interactions: 61984
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 103 "
            pdb=" O   ASN A 107 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" O   SER A 690 "
            pdb=" OG  SER A 690 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   SER A 689 "
            pdb=" OG  SER A 689 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   SER A 154 "
            pdb=" OG  SER A 154 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" NH2 ARG A 513 "
            pdb=" OG  SER A 631 "
     model   vdw
     2.348 3.120
  ... (remaining 61979 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:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.280
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
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      :  0.007   0.089   8716  Z= 0.452
  Angle     :  0.783  11.951  11774  Z= 0.350
  Chirality :  0.043   0.238   1368
  Planarity :  0.004   0.032   1467
  Dihedral  : 13.275  85.555   3236
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.23), residues: 1078
  helix: -0.00 (0.22), residues: 467
  sheet: -1.77 (0.36), residues: 149
  loop : -1.98 (0.24), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 787 
 HIS   0.008   0.001   HIS A 595 
 PHE   0.016   0.001   PHE A 405 
 TYR   0.008   0.001   TYR A 625 
 ARG   0.003   0.000   ARG A 588 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.937 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.2240
  time to fit residues: 14.3795
Evaluate side-chains
  25 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:    0.3980
   chunk 43 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:   20.0000
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
A 327 ASN
A 533 HIS
A 620 ASN
A 776 HIS
A 987 ASN
A1089 GLN
A1122 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.057319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.044460 restraints weight = 33826.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.046231 restraints weight = 15324.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.047442 restraints weight = 9446.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8716  Z= 0.219
  Angle     :  0.507   6.994  11774  Z= 0.263
  Chirality :  0.039   0.147   1368
  Planarity :  0.003   0.029   1467
  Dihedral  :  7.984  57.714   1318
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  9.59 %
    Favored  : 89.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.25), residues: 1078
  helix:  1.41 (0.24), residues: 479
  sheet: -1.35 (0.38), residues: 146
  loop : -1.45 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 558 
 HIS   0.006   0.001   HIS A 595 
 PHE   0.016   0.001   PHE A 226 
 TYR   0.009   0.001   TYR A1004 
 ARG   0.003   0.000   ARG A 175 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.980 
Fit side-chains
REVERT: A  449 MET cc_start: 0.8457 (tpp) cc_final: 0.7581 (tpp)
REVERT: A  453 MET cc_start: 0.8510 (mtp) cc_final: 0.8107 (mpp)
REVERT: A 1136 MET cc_start: 0.8950 (mmm) cc_final: 0.8673 (mmm)
  outliers start: 4
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1753
  time to fit residues: 8.7317
Evaluate side-chains
  28 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  412 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 72 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   chunk 102 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    2.2186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.056120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.043166 restraints weight = 34402.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.044908 restraints weight = 15696.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.046078 restraints weight = 9740.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8716  Z= 0.264
  Angle     :  0.503   6.004  11774  Z= 0.262
  Chirality :  0.039   0.144   1368
  Planarity :  0.003   0.028   1467
  Dihedral  :  6.906  56.986   1318
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 12.26 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.25), residues: 1078
  helix:  1.90 (0.24), residues: 481
  sheet: -1.25 (0.38), residues: 146
  loop : -1.33 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 787 
 HIS   0.005   0.001   HIS A 595 
 PHE   0.015   0.001   PHE A 405 
 TYR   0.008   0.001   TYR A1004 
 ARG   0.002   0.000   ARG A 588 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A  449 MET cc_start: 0.8472 (tpp) cc_final: 0.7602 (tpp)
REVERT: A  453 MET cc_start: 0.8450 (mtp) cc_final: 0.8026 (mpp)
REVERT: A 1136 MET cc_start: 0.8977 (mmm) cc_final: 0.8686 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 30
  average time/residue: 0.1757
  time to fit residues: 8.8725
Evaluate side-chains
  26 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 101 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0670
   chunk 46 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 595 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.057669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.044731 restraints weight = 33611.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.046513 restraints weight = 15367.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.047754 restraints weight = 9520.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8716  Z= 0.150
  Angle     :  0.449   5.747  11774  Z= 0.232
  Chirality :  0.038   0.144   1368
  Planarity :  0.003   0.027   1467
  Dihedral  :  5.876  51.695   1318
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 13.94 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1078
  helix:  2.28 (0.24), residues: 482
  sheet: -1.03 (0.39), residues: 146
  loop : -1.16 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 558 
 HIS   0.004   0.001   HIS A 595 
 PHE   0.013   0.001   PHE A 405 
 TYR   0.009   0.001   TYR A1004 
 ARG   0.002   0.000   ARG A 588 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.979 
Fit side-chains
REVERT: A  186 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9017 (mm)
REVERT: A  249 MET cc_start: 0.9024 (mtp) cc_final: 0.8699 (mtm)
REVERT: A  449 MET cc_start: 0.8356 (tpp) cc_final: 0.7470 (tpp)
REVERT: A  453 MET cc_start: 0.8503 (mtp) cc_final: 0.8083 (mpp)
REVERT: A 1136 MET cc_start: 0.8990 (mmm) cc_final: 0.8711 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 32
  average time/residue: 0.1990
  time to fit residues: 10.2312
Evaluate side-chains
  29 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  685 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.057517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.044596 restraints weight = 33767.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.046396 restraints weight = 15430.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.047624 restraints weight = 9500.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8716  Z= 0.166
  Angle     :  0.451   6.272  11774  Z= 0.231
  Chirality :  0.038   0.145   1368
  Planarity :  0.003   0.025   1467
  Dihedral  :  5.588  50.958   1318
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 14.27 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.26), residues: 1078
  helix:  2.44 (0.24), residues: 482
  sheet: -0.89 (0.40), residues: 146
  loop : -1.06 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 787 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.013   0.001   PHE A 405 
 TYR   0.010   0.001   TYR A 992 
 ARG   0.003   0.000   ARG A 239 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  239 ARG cc_start: 0.9326 (tpp80) cc_final: 0.8932 (tpt170)
REVERT: A  249 MET cc_start: 0.9026 (mtp) cc_final: 0.8701 (mtm)
REVERT: A  449 MET cc_start: 0.8398 (tpp) cc_final: 0.7545 (tpp)
REVERT: A  453 MET cc_start: 0.8491 (mtp) cc_final: 0.8077 (mpp)
REVERT: A 1136 MET cc_start: 0.8978 (mmm) cc_final: 0.8690 (mmm)
  outliers start: 9
  outliers final: 3
  residues processed: 35
  average time/residue: 0.1929
  time to fit residues: 10.8527
Evaluate side-chains
  30 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  829 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 33 optimal weight:    0.3980
   chunk 52 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.056926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.043978 restraints weight = 33719.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.045750 restraints weight = 15545.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.046953 restraints weight = 9651.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8716  Z= 0.188
  Angle     :  0.461   6.371  11774  Z= 0.236
  Chirality :  0.038   0.144   1368
  Planarity :  0.003   0.025   1467
  Dihedral  :  5.464  50.495   1318
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 14.49 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1078
  helix:  2.51 (0.24), residues: 483
  sheet: -0.77 (0.41), residues: 146
  loop : -0.99 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 787 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.014   0.001   PHE A 405 
 TYR   0.009   0.001   TYR A1004 
 ARG   0.003   0.000   ARG A 239 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 27
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  186 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: A  196 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8706 (t-90)
REVERT: A  239 ARG cc_start: 0.9356 (tpp80) cc_final: 0.9009 (ttp80)
REVERT: A  249 MET cc_start: 0.9028 (mtp) cc_final: 0.8711 (mtm)
REVERT: A  449 MET cc_start: 0.8513 (tpp) cc_final: 0.7659 (tpp)
REVERT: A  453 MET cc_start: 0.8497 (mtp) cc_final: 0.8077 (mpp)
REVERT: A 1136 MET cc_start: 0.8999 (mmm) cc_final: 0.8716 (mmm)
REVERT: A 1167 MET cc_start: 0.8942 (mtm) cc_final: 0.8665 (mtt)
  outliers start: 13
  outliers final: 7
  residues processed: 38
  average time/residue: 0.1843
  time to fit residues: 11.1115
Evaluate side-chains
  36 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  685 MET
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1103 THR
Chi-restraints excluded: chain A residue 1182 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 105 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 96 optimal weight:    0.3980
   chunk 80 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    2.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.056887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.044082 restraints weight = 34178.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.045835 restraints weight = 15734.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.047032 restraints weight = 9779.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8716  Z= 0.264
  Angle     :  0.501   6.821  11774  Z= 0.257
  Chirality :  0.039   0.142   1368
  Planarity :  0.003   0.027   1467
  Dihedral  :  5.634  49.882   1318
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.38 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1078
  helix:  2.51 (0.24), residues: 482
  sheet: -0.91 (0.40), residues: 151
  loop : -0.98 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 787 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.013   0.001   PHE A 405 
 TYR   0.008   0.001   TYR A1004 
 ARG   0.002   0.000   ARG A 239 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 26
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A  249 MET cc_start: 0.9099 (mtp) cc_final: 0.8559 (mpp)
REVERT: A  449 MET cc_start: 0.8573 (tpp) cc_final: 0.7701 (tpp)
REVERT: A  453 MET cc_start: 0.8447 (mtp) cc_final: 0.8063 (mpp)
REVERT: A 1136 MET cc_start: 0.9069 (mmm) cc_final: 0.8815 (mmm)
  outliers start: 11
  outliers final: 5
  residues processed: 36
  average time/residue: 0.1539
  time to fit residues: 9.6740
Evaluate side-chains
  31 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  685 MET
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1103 THR
Chi-restraints excluded: chain A residue 1182 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 53 optimal weight:    0.2980
   chunk 63 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 83 optimal weight:    0.3980
   chunk 87 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 98 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.059198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.046558 restraints weight = 34012.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.048398 restraints weight = 15342.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.049637 restraints weight = 9366.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8716  Z= 0.126
  Angle     :  0.453   8.014  11774  Z= 0.229
  Chirality :  0.038   0.157   1368
  Planarity :  0.003   0.028   1467
  Dihedral  :  5.214  51.476   1318
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 16.50 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.26), residues: 1078
  helix:  2.65 (0.24), residues: 482
  sheet: -0.80 (0.41), residues: 150
  loop : -0.87 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 558 
 HIS   0.003   0.001   HIS A1069 
 PHE   0.012   0.001   PHE A 405 
 TYR   0.010   0.001   TYR A1004 
 ARG   0.003   0.000   ARG A 239 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  196 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8686 (t-90)
REVERT: A  239 ARG cc_start: 0.9344 (tpp80) cc_final: 0.9010 (ttp80)
REVERT: A  249 MET cc_start: 0.9088 (mtp) cc_final: 0.8544 (mpp)
REVERT: A  449 MET cc_start: 0.8429 (tpp) cc_final: 0.7529 (tpp)
REVERT: A  453 MET cc_start: 0.8482 (mtp) cc_final: 0.8079 (mpp)
REVERT: A 1136 MET cc_start: 0.9112 (mmm) cc_final: 0.8593 (mmm)
REVERT: A 1167 MET cc_start: 0.8865 (mtm) cc_final: 0.8602 (mtt)
  outliers start: 4
  outliers final: 2
  residues processed: 33
  average time/residue: 0.1906
  time to fit residues: 9.9928
Evaluate side-chains
  31 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  498 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 46 optimal weight:    0.6980
   chunk 64 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 101 optimal weight:    0.9980
   chunk 55 optimal weight:    0.4980
   chunk 75 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.058120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.045370 restraints weight = 33968.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.047163 restraints weight = 15524.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.048376 restraints weight = 9570.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8716  Z= 0.188
  Angle     :  0.468   8.944  11774  Z= 0.237
  Chirality :  0.038   0.148   1368
  Planarity :  0.003   0.028   1467
  Dihedral  :  5.230  50.271   1318
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 16.83 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.26), residues: 1078
  helix:  2.70 (0.24), residues: 483
  sheet: -0.77 (0.41), residues: 151
  loop : -0.84 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 787 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.013   0.001   PHE A 405 
 TYR   0.008   0.001   TYR A1004 
 ARG   0.002   0.000   ARG A 239 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 1.429 
Fit side-chains
REVERT: A  196 HIS cc_start: 0.9178 (OUTLIER) cc_final: 0.8319 (t-90)
REVERT: A  249 MET cc_start: 0.9092 (mtp) cc_final: 0.8542 (mpp)
REVERT: A  449 MET cc_start: 0.8519 (tpp) cc_final: 0.7660 (tpp)
REVERT: A  453 MET cc_start: 0.8462 (mtp) cc_final: 0.8075 (mpp)
REVERT: A 1136 MET cc_start: 0.9156 (mmm) cc_final: 0.8937 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 31
  average time/residue: 0.1876
  time to fit residues: 10.7639
Evaluate side-chains
  30 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue 1103 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 57 optimal weight:    8.9990
   chunk 80 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.056591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.043790 restraints weight = 34188.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.045532 restraints weight = 15775.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.046710 restraints weight = 9813.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8716  Z= 0.280
  Angle     :  0.517   8.546  11774  Z= 0.264
  Chirality :  0.040   0.179   1368
  Planarity :  0.003   0.027   1467
  Dihedral  :  5.595  49.220   1318
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 16.83 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.26), residues: 1078
  helix:  2.61 (0.24), residues: 482
  sheet: -0.84 (0.40), residues: 151
  loop : -0.85 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 218 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.014   0.001   PHE A 405 
 TYR   0.009   0.001   TYR A 625 
 ARG   0.002   0.000   ARG A 239 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A  196 HIS cc_start: 0.9191 (OUTLIER) cc_final: 0.8257 (t-90)
REVERT: A  401 MET cc_start: 0.8817 (mmp) cc_final: 0.8412 (mmm)
REVERT: A  449 MET cc_start: 0.8610 (tpp) cc_final: 0.7706 (tpp)
REVERT: A  453 MET cc_start: 0.8433 (mtp) cc_final: 0.8064 (mpp)
REVERT: A 1136 MET cc_start: 0.9166 (mmm) cc_final: 0.8935 (mmm)
  outliers start: 7
  outliers final: 4
  residues processed: 33
  average time/residue: 0.1758
  time to fit residues: 9.9073
Evaluate side-chains
  31 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1103 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 50 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 72 optimal weight:    0.3980
   chunk 76 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.057535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.044724 restraints weight = 34290.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.046503 restraints weight = 15695.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.047714 restraints weight = 9697.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8716  Z= 0.189
  Angle     :  0.479   9.389  11774  Z= 0.244
  Chirality :  0.039   0.162   1368
  Planarity :  0.003   0.028   1467
  Dihedral  :  5.436  49.938   1318
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 17.17 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.26), residues: 1078
  helix:  2.67 (0.24), residues: 482
  sheet: -0.81 (0.41), residues: 150
  loop : -0.81 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 218 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.012   0.001   PHE A 405 
 TYR   0.009   0.001   TYR A1004 
 ARG   0.002   0.000   ARG A 239 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2471.07 seconds
wall clock time: 44 minutes 56.88 seconds (2696.88 seconds total)