Starting phenix.real_space_refine
on Sat Aug 23 02:14:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xmp_22260/08_2025/6xmp_22260_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xmp_22260/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xmp_22260/08_2025/6xmp_22260_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xmp_22260/08_2025/6xmp_22260_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xmp_22260/08_2025/6xmp_22260.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xmp_22260/08_2025/6xmp_22260.map"
  }
  resolution = 3.5
  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=   0.060
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 7, 'ARG:plan': 5, 'ASN:plan1': 2, 'TYR:plan': 1}
          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: 2.01, per 1000 atoms: 0.24
  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: 0.66
  Conformation dependent library (CDL) restraints added in 319.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.37
  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: 1.65

  Time building geometry restraints manager: 0.90 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:             1.140
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.320
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.050
-------------------------------------------------------------------------------
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= 0.355
  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 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: -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
 ARG   0.003   0.000   ARG A 588 
 TYR   0.008   0.001   TYR A 625 
 PHE   0.016   0.001   PHE A 405 
 TRP   0.005   0.001   TRP A 787 
 HIS   0.008   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00735 ( 8716)
  covalent geometry    : angle       0.78283 (11774)
  hydrogen bonds       : bond        0.16604 (  405)
  hydrogen bonds       : angle       6.05405 ( 1185)

*********************** 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  : 0.338 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0877
  time to fit residues: 5.5211
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  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 138 HIS
A 327 ASN
A 533 HIS
A 620 ASN
A 776 HIS
A 987 ASN
A1089 GLN
A1122 GLN
A1159 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.058743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.045615 restraints weight = 33766.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.047473 restraints weight = 15172.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.048730 restraints weight = 9278.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.049539 restraints weight = 6750.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.050129 restraints weight = 5482.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8716  Z= 0.103
  Angle     :  0.484   7.144  11774  Z= 0.248
  Chirality :  0.038   0.140   1368
  Planarity :  0.003   0.028   1467
  Dihedral  :  7.811  56.808   1318
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  7.80 %
    Favored  : 91.75 %
  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: 1078
  helix:  1.46 (0.24), residues: 473
  sheet: -1.28 (0.38), residues: 146
  loop : -1.51 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 175 
 TYR   0.009   0.001   TYR A1004 
 PHE   0.015   0.001   PHE A 226 
 TRP   0.008   0.001   TRP A 558 
 HIS   0.006   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 8716)
  covalent geometry    : angle       0.48429 (11774)
  hydrogen bonds       : bond        0.04478 (  405)
  hydrogen bonds       : angle       4.20824 ( 1185)

*********************** 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
  33 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  249 MET cc_start: 0.8938 (mtp) cc_final: 0.8347 (mpp)
REVERT: A 1136 MET cc_start: 0.8963 (mmm) cc_final: 0.8651 (mmm)
  outliers start: 4
  outliers final: 3
  residues processed: 33
  average time/residue: 0.0867
  time to fit residues: 4.4093
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  : 0.343 
-------------------------------------------------------------------------------
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 10 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 75 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 82 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0070
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 = 0.3162 r_free = 0.3162 target = 0.059383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.046663 restraints weight = 33373.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.048495 restraints weight = 14940.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.049752 restraints weight = 9147.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.050596 restraints weight = 6621.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.051142 restraints weight = 5304.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1365

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= 0.089
  Angle     :  0.453   5.893  11774  Z= 0.231
  Chirality :  0.038   0.143   1368
  Planarity :  0.003   0.027   1467
  Dihedral  :  6.532  57.805   1318
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.14 %
    Favored  : 89.41 %
  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:  0.43 (0.25), residues: 1078
  helix:  2.02 (0.24), residues: 481
  sheet: -0.98 (0.39), residues: 146
  loop : -1.20 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 239 
 TYR   0.008   0.001   TYR A1004 
 PHE   0.012   0.001   PHE A 405 
 TRP   0.006   0.001   TRP A 558 
 HIS   0.004   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 8716)
  covalent geometry    : angle       0.45318 (11774)
  hydrogen bonds       : bond        0.03885 (  405)
  hydrogen bonds       : angle       3.83390 ( 1185)

*********************** 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
  33 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  239 ARG cc_start: 0.9347 (tpp80) cc_final: 0.8936 (tpt170)
REVERT: A  249 MET cc_start: 0.8928 (mtp) cc_final: 0.8335 (mpp)
REVERT: A  453 MET cc_start: 0.8621 (mtp) cc_final: 0.8190 (mpp)
REVERT: A 1136 MET cc_start: 0.8996 (mmm) cc_final: 0.8652 (mmm)
  outliers start: 4
  outliers final: 3
  residues processed: 33
  average time/residue: 0.0832
  time to fit residues: 4.3446
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  : 0.321 
-------------------------------------------------------------------------------
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  829 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    9.9990
   chunk 63 optimal weight:    0.0170
   chunk 34 optimal weight:    0.0270
   chunk 26 optimal weight:    0.5980
   chunk 83 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.3280

-------------------------------------------------------------------------------
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 = 0.3131 r_free = 0.3131 target = 0.057971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.045064 restraints weight = 34269.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.046863 restraints weight = 15495.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.048095 restraints weight = 9493.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.048932 restraints weight = 6903.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.049464 restraints weight = 5560.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8716  Z= 0.118
  Angle     :  0.461   5.901  11774  Z= 0.236
  Chirality :  0.038   0.143   1368
  Planarity :  0.003   0.025   1467
  Dihedral  :  5.903  52.177   1318
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 11.82 %
    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 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 (0.26), residues: 1078
  helix:  2.29 (0.24), residues: 483
  sheet: -0.87 (0.39), residues: 146
  loop : -1.09 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 239 
 TYR   0.008   0.001   TYR A1004 
 PHE   0.013   0.001   PHE A 405 
 TRP   0.004   0.001   TRP A 787 
 HIS   0.004   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8716)
  covalent geometry    : angle       0.46127 (11774)
  hydrogen bonds       : bond        0.04220 (  405)
  hydrogen bonds       : angle       3.72213 ( 1185)

*********************** 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
  36 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A  186 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9035 (mm)
REVERT: A  453 MET cc_start: 0.8595 (mtp) cc_final: 0.8170 (mpp)
REVERT: A 1136 MET cc_start: 0.8977 (mmm) cc_final: 0.8635 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 35
  average time/residue: 0.0803
  time to fit residues: 4.5089
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  : 0.333 
-------------------------------------------------------------------------------
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  685 MET
Chi-restraints excluded: chain A residue  829 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 80 optimal weight:    0.0370
   chunk 30 optimal weight:   20.0000
   chunk 71 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0870
   chunk 0 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    2.0242

-------------------------------------------------------------------------------
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 = 0.3099 r_free = 0.3099 target = 0.056547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.043562 restraints weight = 34325.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.045333 restraints weight = 15817.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.046531 restraints weight = 9758.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.047313 restraints weight = 7147.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.047863 restraints weight = 5831.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8716  Z= 0.160
  Angle     :  0.497   8.936  11774  Z= 0.253
  Chirality :  0.039   0.143   1368
  Planarity :  0.003   0.025   1467
  Dihedral  :  5.692  50.982   1318
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.27 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.26), residues: 1078
  helix:  2.41 (0.24), residues: 483
  sheet: -0.86 (0.40), residues: 146
  loop : -1.05 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 239 
 TYR   0.008   0.001   TYR A1004 
 PHE   0.013   0.001   PHE A 405 
 TRP   0.005   0.001   TRP A 218 
 HIS   0.004   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8716)
  covalent geometry    : angle       0.49668 (11774)
  hydrogen bonds       : bond        0.04694 (  405)
  hydrogen bonds       : angle       3.84807 ( 1185)

*********************** 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
  34 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 25
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  453 MET cc_start: 0.8586 (mtp) cc_final: 0.8162 (mpp)
REVERT: A 1136 MET cc_start: 0.8989 (mmm) cc_final: 0.8662 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 33
  average time/residue: 0.0686
  time to fit residues: 3.8812
Evaluate side-chains
  30 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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  498 VAL
Chi-restraints excluded: chain A residue  685 MET
Chi-restraints excluded: chain A residue 1072 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0970
   chunk 66 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.058191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.045305 restraints weight = 33698.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.047125 restraints weight = 15330.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.048365 restraints weight = 9416.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.049202 restraints weight = 6856.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.049752 restraints weight = 5527.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8716  Z= 0.090
  Angle     :  0.452   7.013  11774  Z= 0.229
  Chirality :  0.038   0.143   1368
  Planarity :  0.003   0.026   1467
  Dihedral  :  5.292  52.124   1318
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 13.49 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1078
  helix:  2.60 (0.24), residues: 482
  sheet: -0.73 (0.41), residues: 146
  loop : -0.97 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 239 
 TYR   0.008   0.001   TYR A1004 
 PHE   0.012   0.001   PHE A 405 
 TRP   0.006   0.001   TRP A 558 
 HIS   0.004   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 8716)
  covalent geometry    : angle       0.45190 (11774)
  hydrogen bonds       : bond        0.03880 (  405)
  hydrogen bonds       : angle       3.58305 ( 1185)

*********************** 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
  36 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  186 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8992 (mm)
REVERT: A  239 ARG cc_start: 0.9353 (tpp80) cc_final: 0.8940 (tpt170)
REVERT: A  453 MET cc_start: 0.8469 (mtp) cc_final: 0.8070 (mpp)
REVERT: A 1136 MET cc_start: 0.9084 (mmm) cc_final: 0.8818 (mmm)
  outliers start: 7
  outliers final: 4
  residues processed: 35
  average time/residue: 0.0836
  time to fit residues: 4.6187
Evaluate side-chains
  32 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue 1103 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0470
   chunk 51 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0170
   chunk 61 optimal weight:    4.9990
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.4116

-------------------------------------------------------------------------------
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 = 0.3162 r_free = 0.3162 target = 0.059299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.046472 restraints weight = 33910.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.048339 restraints weight = 15345.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.049605 restraints weight = 9350.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.050407 restraints weight = 6788.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.051001 restraints weight = 5489.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8716  Z= 0.080
  Angle     :  0.451   8.834  11774  Z= 0.224
  Chirality :  0.037   0.142   1368
  Planarity :  0.003   0.027   1467
  Dihedral  :  4.953  52.186   1318
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.27 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.26), residues: 1078
  helix:  2.73 (0.24), residues: 486
  sheet: -0.64 (0.41), residues: 151
  loop : -0.84 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 239 
 TYR   0.007   0.001   TYR A1004 
 PHE   0.010   0.001   PHE A 405 
 TRP   0.007   0.001   TRP A 558 
 HIS   0.003   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00170 ( 8716)
  covalent geometry    : angle       0.45052 (11774)
  hydrogen bonds       : bond        0.03415 (  405)
  hydrogen bonds       : angle       3.43391 ( 1185)

*********************** 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
  39 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  186 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8996 (mm)
REVERT: A  239 ARG cc_start: 0.9353 (tpp80) cc_final: 0.8955 (tpt170)
REVERT: A  453 MET cc_start: 0.8418 (mtp) cc_final: 0.8026 (mpp)
REVERT: A 1136 MET cc_start: 0.9062 (mmm) cc_final: 0.8803 (mmm)
  outliers start: 7
  outliers final: 6
  residues processed: 38
  average time/residue: 0.0833
  time to fit residues: 4.9716
Evaluate side-chains
  37 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1103 THR
Chi-restraints excluded: chain A residue 1180 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 99 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0040
   chunk 95 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    1.1196

-------------------------------------------------------------------------------
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 = 0.3133 r_free = 0.3133 target = 0.058066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.045249 restraints weight = 33815.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.047052 restraints weight = 15366.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.048299 restraints weight = 9436.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.049142 restraints weight = 6854.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.049701 restraints weight = 5521.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8716  Z= 0.104
  Angle     :  0.454   7.918  11774  Z= 0.228
  Chirality :  0.038   0.142   1368
  Planarity :  0.003   0.027   1467
  Dihedral  :  4.970  51.474   1318
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 14.60 %
    Favored  : 84.50 %
  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:  1.31 (0.26), residues: 1078
  helix:  2.77 (0.24), residues: 486
  sheet: -0.63 (0.41), residues: 151
  loop : -0.79 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 239 
 TYR   0.007   0.001   TYR A1004 
 PHE   0.018   0.001   PHE A 226 
 TRP   0.005   0.001   TRP A 787 
 HIS   0.003   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8716)
  covalent geometry    : angle       0.45361 (11774)
  hydrogen bonds       : bond        0.03802 (  405)
  hydrogen bonds       : angle       3.48383 ( 1185)

*********************** 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
  36 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  453 MET cc_start: 0.8452 (mtp) cc_final: 0.8054 (mpp)
REVERT: A 1136 MET cc_start: 0.9068 (mmm) cc_final: 0.8796 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 35
  average time/residue: 0.0849
  time to fit residues: 4.6776
Evaluate side-chains
  33 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
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  685 MET
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1103 THR
Chi-restraints excluded: chain A residue 1180 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 13 optimal weight:    0.3980
   chunk 46 optimal weight:    0.0980
   chunk 50 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3155 r_free = 0.3155 target = 0.058946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.046346 restraints weight = 32729.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.048199 restraints weight = 14314.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.049491 restraints weight = 8572.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.050310 restraints weight = 6107.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.050917 restraints weight = 4890.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8716  Z= 0.082
  Angle     :  0.459  10.459  11774  Z= 0.226
  Chirality :  0.037   0.140   1368
  Planarity :  0.003   0.027   1467
  Dihedral  :  4.827  52.153   1318
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 14.60 %
    Favored  : 84.50 %
  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:  1.38 (0.27), residues: 1078
  helix:  2.81 (0.24), residues: 487
  sheet: -0.52 (0.42), residues: 150
  loop : -0.77 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 239 
 TYR   0.007   0.001   TYR A1004 
 PHE   0.017   0.001   PHE A 226 
 TRP   0.007   0.001   TRP A 558 
 HIS   0.003   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00177 ( 8716)
  covalent geometry    : angle       0.45854 (11774)
  hydrogen bonds       : bond        0.03454 (  405)
  hydrogen bonds       : angle       3.41629 ( 1185)

*********************** 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
  37 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  196 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.8303 (t-90)
REVERT: A  401 MET cc_start: 0.8818 (mmp) cc_final: 0.8395 (mmm)
REVERT: A  453 MET cc_start: 0.8403 (mtp) cc_final: 0.8013 (mpp)
REVERT: A 1136 MET cc_start: 0.9015 (mmm) cc_final: 0.8770 (mmm)
  outliers start: 8
  outliers final: 7
  residues processed: 36
  average time/residue: 0.0653
  time to fit residues: 4.0336
Evaluate side-chains
  37 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  196 HIS
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 1072 THR
Chi-restraints excluded: chain A residue 1103 THR
Chi-restraints excluded: chain A residue 1180 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 105 optimal weight:    0.3980
   chunk 72 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 83 optimal weight:    0.3980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3153 r_free = 0.3153 target = 0.058851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.046231 restraints weight = 32872.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.048075 restraints weight = 14402.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.049344 restraints weight = 8629.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.050221 restraints weight = 6183.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.050806 restraints weight = 4894.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8716  Z= 0.086
  Angle     :  0.452   9.382  11774  Z= 0.224
  Chirality :  0.037   0.140   1368
  Planarity :  0.003   0.027   1467
  Dihedral  :  4.749  51.943   1318
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 14.60 %
    Favored  : 84.50 %
  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:  1.45 (0.27), residues: 1078
  helix:  2.86 (0.24), residues: 487
  sheet: -0.45 (0.42), residues: 150
  loop : -0.73 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 239 
 TYR   0.007   0.001   TYR A1004 
 PHE   0.016   0.001   PHE A 226 
 TRP   0.005   0.001   TRP A 558 
 HIS   0.003   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 8716)
  covalent geometry    : angle       0.45224 (11774)
  hydrogen bonds       : bond        0.03484 (  405)
  hydrogen bonds       : angle       3.40296 ( 1185)

********************** 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
  37 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  196 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8310 (t-90)
REVERT: A  401 MET cc_start: 0.8824 (mmp) cc_final: 0.8397 (mmm)
REVERT: A  453 MET cc_start: 0.8396 (mtp) cc_final: 0.7997 (mpp)
REVERT: A 1136 MET cc_start: 0.9053 (mmm) cc_final: 0.8780 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 36
  average time/residue: 0.0691
  time to fit residues: 4.2535
Evaluate side-chains
  36 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1103 THR
Chi-restraints excluded: chain A residue 1180 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0770
   chunk 36 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7138

-------------------------------------------------------------------------------
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 = 0.3157 r_free = 0.3157 target = 0.059011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.046324 restraints weight = 32905.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.048197 restraints weight = 14532.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.049470 restraints weight = 8688.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.050342 restraints weight = 6217.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.050885 restraints weight = 4933.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8716  Z= 0.085
  Angle     :  0.450   9.599  11774  Z= 0.223
  Chirality :  0.037   0.139   1368
  Planarity :  0.003   0.027   1467
  Dihedral  :  4.708  52.046   1318
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 15.05 %
    Favored  : 84.17 %
  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:  1.49 (0.27), residues: 1078
  helix:  2.88 (0.24), residues: 488
  sheet: -0.42 (0.42), residues: 150
  loop : -0.71 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 239 
 TYR   0.007   0.001   TYR A1004 
 PHE   0.016   0.001   PHE A 226 
 TRP   0.006   0.000   TRP A 558 
 HIS   0.003   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 ( 8716)
  covalent geometry    : angle       0.45039 (11774)
  hydrogen bonds       : bond        0.03449 (  405)
  hydrogen bonds       : angle       3.38399 ( 1185)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1304.85 seconds
wall clock time: 23 minutes 19.09 seconds (1399.09 seconds total)