Starting phenix.real_space_refine
on Tue Jan 14 23:18:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     P       3      5.49       5
     S      38      5.16       5
     C    4854      2.51       5
     N    1327      2.21       5
     O    1287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 7511
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 993, 7478
          Classifications: {'peptide': 993}
          Incomplete info: {'truncation_to_alanine': 108}
          Link IDs: {'PTRANS': 43, 'TRANS': 949}
          Chain breaks: 8
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 411
          Unresolved non-hydrogen angles: 510
          Unresolved non-hydrogen dihedrals: 333
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 285
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' CA': 2, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.42, per 1000 atoms: 0.72
  Number of scatterers: 7511
  At special positions: 0
  Unit cell: (87.768, 120.06, 153.18, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      2     19.99
     S      38     16.00
     P       3     15.00
     O    1287      8.00
     N    1327      7.00
     C    4854      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 993 " - pdb=" SG  CYS A1011 " distance=2.59

  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: 2.72
  Conformation dependent library (CDL) restraints added in 976.5 milliseconds
  

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1840

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 4 sheets defined
      67.7% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 9
      No H-bonds generated for 'chain 'A' and resid 7 through 9'
    Processing helix  chain 'A' and resid 10 through 15
      removed outlier: 3.650A  pdb=" N   ILE A  14 " --> pdb=" O   TRP A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 109
      removed outlier: 3.884A  pdb=" N   VAL A 102 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 150
      removed outlier: 3.724A  pdb=" N   VAL A 143 " --> pdb=" O   ARG A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 176
    Processing helix  chain 'A' and resid 246 through 259
    Processing helix  chain 'A' and resid 264 through 268
      removed outlier: 3.951A  pdb=" N   GLY A 268 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 294
    Processing helix  chain 'A' and resid 308 through 318
    Processing helix  chain 'A' and resid 327 through 336
    Processing helix  chain 'A' and resid 344 through 357
      removed outlier: 4.294A  pdb=" N   GLN A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 386
      removed outlier: 3.508A  pdb=" N   GLY A 386 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 403
    Processing helix  chain 'A' and resid 406 through 413
    Processing helix  chain 'A' and resid 421 through 435
      removed outlier: 4.076A  pdb=" N   ALA A 427 " --> pdb=" O   PHE A 423 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER A 428 " --> pdb=" O   HIS A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 447
    Processing helix  chain 'A' and resid 450 through 455
    Processing helix  chain 'A' and resid 456 through 466
    Processing helix  chain 'A' and resid 471 through 480
    Processing helix  chain 'A' and resid 502 through 512
      removed outlier: 3.589A  pdb=" N   VAL A 506 " --> pdb=" O   ASP A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 570
    Processing helix  chain 'A' and resid 571 through 582
    Processing helix  chain 'A' and resid 584 through 603
    Processing helix  chain 'A' and resid 607 through 634
      removed outlier: 3.645A  pdb=" N   ARG A 611 " --> pdb=" O   GLU A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 645
      removed outlier: 3.541A  pdb=" N   LEU A 643 " --> pdb=" O   ALA A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 662
    Processing helix  chain 'A' and resid 663 through 668
    Processing helix  chain 'A' and resid 669 through 681
    Processing helix  chain 'A' and resid 689 through 699
    Processing helix  chain 'A' and resid 700 through 705
      removed outlier: 3.557A  pdb=" N   THR A 705 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 778
      removed outlier: 3.526A  pdb=" N   ALA A 778 " --> pdb=" O   HIS A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 803
    Processing helix  chain 'A' and resid 811 through 834
    Processing helix  chain 'A' and resid 852 through 862
      removed outlier: 3.847A  pdb=" N   ASP A 862 " --> pdb=" O   LEU A 858 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 884
    Processing helix  chain 'A' and resid 887 through 905
    Processing helix  chain 'A' and resid 906 through 912
    Processing helix  chain 'A' and resid 916 through 926
    Processing helix  chain 'A' and resid 926 through 953
    Processing helix  chain 'A' and resid 958 through 967
    Processing helix  chain 'A' and resid 967 through 974
      removed outlier: 3.624A  pdb=" N   ILE A 974 " --> pdb=" O   PRO A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 983
    Processing helix  chain 'A' and resid 984 through 988
    Processing helix  chain 'A' and resid 1016 through 1033
      removed outlier: 3.883A  pdb=" N   VAL A1020 " --> pdb=" O   ALA A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1033 through 1071
      removed outlier: 4.877A  pdb=" N   GLY A1052 " --> pdb=" O   GLY A1048 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   ASN A1053 " --> pdb=" O   LYS A1049 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   TYR A1063 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ARG A1064 " --> pdb=" O   ALA A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1088
      removed outlier: 4.267A  pdb=" N   SER A1083 " --> pdb=" O   PHE A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1116 through 1143
    Processing helix  chain 'A' and resid 1143 through 1176
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19
    Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 156
      removed outlier: 6.165A  pdb=" N   THR A 155 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   GLY A 187 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   VAL A 235 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ALA A 189 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ASN A  89 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   LEU A 234 " --> pdb=" O   ASN A  89 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LEU A  91 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ASP A 236 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   LEU A  93 " --> pdb=" O   ASP A 236 " (cutoff:3.500A)
      removed outlier: 7.680A  pdb=" N   TYR A 211 " --> pdb=" O   GLU A  77 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   ASP A  79 " --> pdb=" O   TYR A 211 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 122
      removed outlier: 6.550A  pdb=" N   VAL A 118 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 7.565A  pdb=" N   LEU A 276 " --> pdb=" O   VAL A 118 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   SER A 120 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   LEU A 299 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LEU A 275 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   VAL A 301 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LEU A 277 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   CYS A 298 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   TYR A 364 " --> pdb=" O   CYS A 298 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   LEU A 300 " --> pdb=" O   TYR A 364 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 991
      removed outlier: 4.062A  pdb=" N   GLU A 989 " --> pdb=" O   HIS A1002 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   TRP A1000 " --> pdb=" O   SER A 991 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1383 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.46

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2433
        1.34 -     1.46: 1693
        1.46 -     1.57: 3494
        1.57 -     1.69: 5
        1.69 -     1.81: 57
  Bond restraints: 7682
  Sorted by residual:
  bond pdb=" CB  THR A 823 "
       pdb=" CG2 THR A 823 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.45e+00
  bond pdb=" CB  TRP A1124 "
       pdb=" CG  TRP A1124 "
    ideal  model  delta    sigma   weight residual
    1.498  1.462  0.036 3.10e-02 1.04e+03 1.34e+00
  bond pdb=" CB  GLN A 669 "
       pdb=" CG  GLN A 669 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.07e+00
  bond pdb=" CB  TRP A 681 "
       pdb=" CG  TRP A 681 "
    ideal  model  delta    sigma   weight residual
    1.498  1.468  0.030 3.10e-02 1.04e+03 9.61e-01
  bond pdb=" CB  CYS A1011 "
       pdb=" SG  CYS A1011 "
    ideal  model  delta    sigma   weight residual
    1.808  1.776  0.032 3.30e-02 9.18e+02 9.17e-01
  ... (remaining 7677 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 10227
        1.27 -     2.55: 171
        2.55 -     3.82: 45
        3.82 -     5.10: 12
        5.10 -     6.37: 4
  Bond angle restraints: 10459
  Sorted by residual:
  angle pdb=" C3' ATP A2003 "
        pdb=" C4' ATP A2003 "
        pdb=" C5' ATP A2003 "
      ideal   model   delta    sigma   weight residual
     115.19  110.95    4.24 1.76e+00 3.23e-01 5.81e+00
  angle pdb=" C2' ATP A2003 "
        pdb=" C3' ATP A2003 "
        pdb=" O3' ATP A2003 "
      ideal   model   delta    sigma   weight residual
     111.83  105.58    6.25 2.67e+00 1.40e-01 5.48e+00
  angle pdb=" N   GLY A 220 "
        pdb=" CA  GLY A 220 "
        pdb=" C   GLY A 220 "
      ideal   model   delta    sigma   weight residual
     110.77  115.28   -4.51 1.93e+00 2.68e-01 5.46e+00
  angle pdb=" C1' ATP A2003 "
        pdb=" C2' ATP A2003 "
        pdb=" O2' ATP A2003 "
      ideal   model   delta    sigma   weight residual
     110.58  104.21    6.37 2.79e+00 1.28e-01 5.20e+00
  angle pdb=" C3' ATP A2003 "
        pdb=" C2' ATP A2003 "
        pdb=" O2' ATP A2003 "
      ideal   model   delta    sigma   weight residual
     111.83  106.09    5.74 2.67e+00 1.40e-01 4.62e+00
  ... (remaining 10454 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 4256
       16.86 -    33.72: 205
       33.72 -    50.59: 41
       50.59 -    67.45: 19
       67.45 -    84.31: 5
  Dihedral angle restraints: 4526
    sinusoidal: 1679
      harmonic: 2847
  Sorted by residual:
  dihedral pdb=" CB  CYS A 993 "
           pdb=" SG  CYS A 993 "
           pdb=" SG  CYS A1011 "
           pdb=" CB  CYS A1011 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.15   60.15     1      1.00e+01 1.00e-02 4.82e+01
  dihedral pdb=" CA  PHE A 207 "
           pdb=" C   PHE A 207 "
           pdb=" N   PRO A 208 "
           pdb=" CA  PRO A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.30   19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  ARG A 139 "
           pdb=" CB  ARG A 139 "
           pdb=" CG  ARG A 139 "
           pdb=" CD  ARG A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.74   58.74     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 4523 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1097
       0.059 -    0.117: 101
       0.117 -    0.176: 5
       0.176 -    0.235: 0
       0.235 -    0.294: 3
  Chirality restraints: 1206
  Sorted by residual:
  chirality pdb=" C2' ATP A2003 "
            pdb=" C1' ATP A2003 "
            pdb=" C3' ATP A2003 "
            pdb=" O2' ATP A2003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.97    0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" C3' ATP A2003 "
            pdb=" C2' ATP A2003 "
            pdb=" C4' ATP A2003 "
            pdb=" O3' ATP A2003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.92    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" C4' ATP A2003 "
            pdb=" C3' ATP A2003 "
            pdb=" C5' ATP A2003 "
            pdb=" O4' ATP A2003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.73    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1203 not shown)

  Planarity restraints: 1315
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 699 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO A 700 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 700 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 700 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A1076 "    0.016 5.00e-02 4.00e+02   2.34e-02 8.79e-01
        pdb=" N   PRO A1077 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO A1077 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A1077 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 456 "   -0.013 5.00e-02 4.00e+02   1.94e-02 6.05e-01
        pdb=" N   PRO A 457 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO A 457 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO A 457 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 1312 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 143
        2.67 -     3.23: 8232
        3.23 -     3.79: 11978
        3.79 -     4.34: 14841
        4.34 -     4.90: 24713
  Nonbonded interactions: 59907
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 828 "
            pdb="CA    CA A2001 "
     model   vdw
     2.119 2.510
  nonbonded pdb=" OE1 GLN A 831 "
            pdb="CA    CA A2001 "
     model   vdw
     2.170 2.510
  nonbonded pdb=" N   GLU A 374 "
            pdb=" OE1 GLU A 374 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   PHE A 454 "
            pdb=" NH1 ARG A 459 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" N   GLU A 389 "
            pdb=" OE1 GLU A 389 "
     model   vdw
     2.238 3.120
  ... (remaining 59902 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 individual isotropic
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:             11.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     21.780
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7682  Z= 0.334
  Angle     :  0.499   6.369  10459  Z= 0.270
  Chirality :  0.036   0.294   1206
  Planarity :  0.003   0.041   1315
  Dihedral  : 11.380  84.310   2683
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  5.79 %
    Favored  : 93.93 %
  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:  1.45 (0.27), residues: 975
  helix:  2.00 (0.21), residues: 605
  sheet: -2.01 (0.59), residues: 59
  loop : -0.46 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 213 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.007   0.001   PHE A 223 
 TYR   0.007   0.001   TYR A1015 
 ARG   0.003   0.000   ARG A1062 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1037 ASN cc_start: 0.8974 (m-40) cc_final: 0.8671 (m110)
REVERT: A 1038 LEU cc_start: 0.9535 (tp) cc_final: 0.9307 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 110
  average time/residue: 0.2000
  time to fit residues: 30.1241
Evaluate side-chains
  66 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  373 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
A1032 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.077004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.060616 restraints weight = 29018.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 4.05
r_work: 0.2982 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7682  Z= 0.205
  Angle     :  0.582  10.997  10459  Z= 0.296
  Chirality :  0.038   0.160   1206
  Planarity :  0.004   0.041   1315
  Dihedral  :  6.966  69.036   1108
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  8.83 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.28), residues: 975
  helix:  2.61 (0.21), residues: 621
  sheet: -1.21 (0.64), residues: 64
  loop : -0.34 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 772 
 HIS   0.002   0.001   HIS A 159 
 PHE   0.022   0.002   PHE A 249 
 TYR   0.010   0.001   TYR A 227 
 ARG   0.010   0.001   ARG A 601 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  784 MET cc_start: 0.9283 (ttm) cc_final: 0.9008 (tmm)
REVERT: A 1034 LEU cc_start: 0.9185 (mp) cc_final: 0.8772 (tt)
REVERT: A 1037 ASN cc_start: 0.9415 (m-40) cc_final: 0.9097 (m110)
REVERT: A 1051 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8418 (tm-30)
  outliers start: 15
  outliers final: 7
  residues processed: 92
  average time/residue: 0.1790
  time to fit residues: 23.5712
Evaluate side-chains
  73 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain A residue  904 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 17 optimal weight:    9.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 165 HIS
A 505 HIS
A 973 GLN
A1032 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.076407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.060054 restraints weight = 29312.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 4.01
r_work: 0.2994 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7682  Z= 0.186
  Angle     :  0.533   9.320  10459  Z= 0.272
  Chirality :  0.036   0.178   1206
  Planarity :  0.004   0.049   1315
  Dihedral  :  6.587  79.120   1108
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.31 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.28), residues: 975
  helix:  2.52 (0.21), residues: 623
  sheet: -1.22 (0.64), residues: 64
  loop : -0.44 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  61 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.021   0.001   PHE A 697 
 TYR   0.009   0.001   TYR A 227 
 ARG   0.007   0.000   ARG A 327 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.8970 (ptp) cc_final: 0.8591 (ptp)
REVERT: A  629 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8246 (tm-30)
REVERT: A 1034 LEU cc_start: 0.9185 (mp) cc_final: 0.8751 (tt)
REVERT: A 1037 ASN cc_start: 0.9369 (m-40) cc_final: 0.9060 (m110)
REVERT: A 1051 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8218 (tm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1618
  time to fit residues: 19.6456
Evaluate side-chains
  74 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  988 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 69 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.075292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.058962 restraints weight = 29260.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 4.05
r_work: 0.2930 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7682  Z= 0.232
  Angle     :  0.527   7.671  10459  Z= 0.268
  Chirality :  0.036   0.148   1206
  Planarity :  0.004   0.042   1315
  Dihedral  :  6.261  86.739   1108
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.87 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.83 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.28), residues: 975
  helix:  2.54 (0.21), residues: 625
  sheet: -1.30 (0.62), residues: 64
  loop : -0.55 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 680 
 HIS   0.005   0.001   HIS A 505 
 PHE   0.025   0.001   PHE A 697 
 TYR   0.009   0.001   TYR A 227 
 ARG   0.005   0.000   ARG A1138 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.9145 (ptp) cc_final: 0.8767 (ptp)
REVERT: A  430 MET cc_start: 0.9607 (tpp) cc_final: 0.9407 (mmm)
REVERT: A  669 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8647 (mm110)
REVERT: A 1034 LEU cc_start: 0.9212 (mp) cc_final: 0.8736 (tt)
REVERT: A 1037 ASN cc_start: 0.9372 (m-40) cc_final: 0.9065 (m110)
REVERT: A 1051 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8266 (tm-30)
  outliers start: 20
  outliers final: 11
  residues processed: 79
  average time/residue: 0.1683
  time to fit residues: 19.5774
Evaluate side-chains
  72 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  988 MET
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   chunk 19 optimal weight:    0.2980
   chunk 48 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 88 optimal weight:    0.2980
   chunk 76 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.076316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.060207 restraints weight = 28738.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 3.98
r_work: 0.2972 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7682  Z= 0.167
  Angle     :  0.514   7.069  10459  Z= 0.259
  Chirality :  0.035   0.152   1206
  Planarity :  0.004   0.038   1315
  Dihedral  :  5.871  87.902   1105
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.36 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 14.21 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.28), residues: 975
  helix:  2.50 (0.21), residues: 633
  sheet: -1.51 (0.60), residues: 70
  loop : -0.62 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 680 
 HIS   0.005   0.001   HIS A 505 
 PHE   0.025   0.001   PHE A 373 
 TYR   0.008   0.001   TYR A 227 
 ARG   0.005   0.000   ARG A1138 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.9125 (ptp) cc_final: 0.8742 (ptp)
REVERT: A  327 ARG cc_start: 0.9199 (tpt170) cc_final: 0.8929 (tmm160)
REVERT: A  574 MET cc_start: 0.9086 (mmt) cc_final: 0.8878 (mmt)
REVERT: A  669 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8643 (mm110)
REVERT: A 1034 LEU cc_start: 0.9186 (mp) cc_final: 0.8719 (tt)
REVERT: A 1037 ASN cc_start: 0.9329 (m-40) cc_final: 0.9030 (m110)
REVERT: A 1051 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8119 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 79
  average time/residue: 0.1595
  time to fit residues: 18.7252
Evaluate side-chains
  73 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  988 MET
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 87 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
A  89 ASN
A 240 HIS
A 908 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.072147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.055642 restraints weight = 29555.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 4.02
r_work: 0.2858 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   7682  Z= 0.389
  Angle     :  0.606   6.735  10459  Z= 0.310
  Chirality :  0.039   0.157   1206
  Planarity :  0.004   0.043   1315
  Dihedral  :  5.763  86.135   1105
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 14.76 %
    Favored  : 82.34 %
  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:  1.89 (0.28), residues: 975
  helix:  2.34 (0.21), residues: 636
  sheet: -1.51 (0.59), residues: 69
  loop : -0.62 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 680 
 HIS   0.004   0.001   HIS A 173 
 PHE   0.022   0.002   PHE A 697 
 TYR   0.012   0.001   TYR A 227 
 ARG   0.004   0.000   ARG A1138 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.9244 (ptp) cc_final: 0.8842 (ptp)
REVERT: A  784 MET cc_start: 0.9235 (ttm) cc_final: 0.8951 (tmm)
REVERT: A 1037 ASN cc_start: 0.9428 (m-40) cc_final: 0.9145 (m110)
REVERT: A 1051 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9369 (ttp80) cc_final: 0.9130 (ttp80)
  outliers start: 21
  outliers final: 15
  residues processed: 70
  average time/residue: 0.1555
  time to fit residues: 16.6286
Evaluate side-chains
  68 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.073959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.057689 restraints weight = 29081.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 3.98
r_work: 0.2930 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7682  Z= 0.182
  Angle     :  0.521   7.983  10459  Z= 0.265
  Chirality :  0.036   0.165   1206
  Planarity :  0.004   0.040   1315
  Dihedral  :  5.559  81.875   1105
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 15.17 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.28), residues: 975
  helix:  2.59 (0.21), residues: 628
  sheet: -1.93 (0.60), residues: 65
  loop : -0.55 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 649 
 HIS   0.003   0.000   HIS A  66 
 PHE   0.017   0.001   PHE A 697 
 TYR   0.008   0.001   TYR A 227 
 ARG   0.009   0.000   ARG A 327 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 61
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8948 (tm-30)
REVERT: A  186 MET cc_start: 0.9191 (ptp) cc_final: 0.8805 (ptp)
REVERT: A  430 MET cc_start: 0.9640 (mmm) cc_final: 0.9275 (tpp)
REVERT: A  669 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8697 (mm110)
REVERT: A  784 MET cc_start: 0.9192 (ttm) cc_final: 0.8913 (tmm)
REVERT: A 1034 LEU cc_start: 0.9229 (mp) cc_final: 0.8727 (tt)
REVERT: A 1037 ASN cc_start: 0.9390 (m-40) cc_final: 0.9090 (m110)
REVERT: A 1051 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9352 (ttp80) cc_final: 0.8807 (ttp80)
  outliers start: 24
  outliers final: 18
  residues processed: 78
  average time/residue: 0.1575
  time to fit residues: 18.5317
Evaluate side-chains
  78 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 75 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 84 optimal weight:    0.1980
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.074169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.057932 restraints weight = 29407.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 4.03
r_work: 0.2934 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7682  Z= 0.194
  Angle     :  0.513   7.720  10459  Z= 0.262
  Chirality :  0.036   0.166   1206
  Planarity :  0.004   0.040   1315
  Dihedral  :  5.400  79.176   1105
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.00 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.28), residues: 975
  helix:  2.62 (0.21), residues: 629
  sheet: -1.89 (0.61), residues: 65
  loop : -0.53 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 772 
 HIS   0.002   0.001   HIS A  66 
 PHE   0.017   0.001   PHE A 697 
 TYR   0.007   0.001   TYR A 818 
 ARG   0.006   0.000   ARG A 327 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8943 (tm-30)
REVERT: A  186 MET cc_start: 0.9169 (ptp) cc_final: 0.8864 (ptp)
REVERT: A  327 ARG cc_start: 0.8732 (tmm160) cc_final: 0.8467 (ttp80)
REVERT: A  629 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: A  669 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8717 (mm110)
REVERT: A  784 MET cc_start: 0.9181 (ttm) cc_final: 0.8912 (tmm)
REVERT: A  983 MET cc_start: 0.9011 (mtt) cc_final: 0.8738 (mtt)
REVERT: A 1034 LEU cc_start: 0.9236 (mp) cc_final: 0.8729 (tt)
REVERT: A 1037 ASN cc_start: 0.9368 (m-40) cc_final: 0.9095 (m110)
REVERT: A 1051 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9369 (ttp80) cc_final: 0.8852 (ttp80)
  outliers start: 21
  outliers final: 14
  residues processed: 76
  average time/residue: 0.1572
  time to fit residues: 17.8009
Evaluate side-chains
  74 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  904 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   chunk 60 optimal weight:    0.2980
   chunk 83 optimal weight:    0.4980
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 72 optimal weight:    0.2980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
A1032 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.075929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.059295 restraints weight = 29732.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 4.22
r_work: 0.2945 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7682  Z= 0.151
  Angle     :  0.504   7.283  10459  Z= 0.258
  Chirality :  0.036   0.186   1206
  Planarity :  0.004   0.039   1315
  Dihedral  :  5.308  76.901   1105
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.59 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.28), residues: 975
  helix:  2.63 (0.21), residues: 630
  sheet: -1.39 (0.60), residues: 70
  loop : -0.62 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 772 
 HIS   0.002   0.000   HIS A  66 
 PHE   0.016   0.001   PHE A 697 
 TYR   0.014   0.001   TYR A 818 
 ARG   0.004   0.000   ARG A1138 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7856 (tm-30)
REVERT: A  135 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8900 (tm-30)
REVERT: A  186 MET cc_start: 0.9166 (ptp) cc_final: 0.8728 (ptp)
REVERT: A  430 MET cc_start: 0.9693 (tpp) cc_final: 0.9481 (mmm)
REVERT: A  629 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8141 (tm-30)
REVERT: A  784 MET cc_start: 0.9141 (ttm) cc_final: 0.8819 (tmm)
REVERT: A  983 MET cc_start: 0.8990 (mtt) cc_final: 0.8706 (mtt)
REVERT: A 1034 LEU cc_start: 0.9182 (mp) cc_final: 0.8673 (tt)
REVERT: A 1051 GLN cc_start: 0.8507 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9334 (ttp80) cc_final: 0.9104 (ttp80)
  outliers start: 20
  outliers final: 17
  residues processed: 78
  average time/residue: 0.1615
  time to fit residues: 18.8820
Evaluate side-chains
  81 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  789 SER
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    0.3980
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
A1032 ASN
A1037 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.074161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.057891 restraints weight = 29951.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 4.02
r_work: 0.2902 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7682  Z= 0.286
  Angle     :  0.546   8.710  10459  Z= 0.280
  Chirality :  0.037   0.184   1206
  Planarity :  0.004   0.041   1315
  Dihedral  :  5.304  76.693   1105
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.00 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.28), residues: 975
  helix:  2.66 (0.21), residues: 629
  sheet: -1.68 (0.63), residues: 64
  loop : -0.65 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 680 
 HIS   0.006   0.001   HIS A 240 
 PHE   0.016   0.001   PHE A 697 
 TYR   0.007   0.001   TYR A 227 
 ARG   0.005   0.000   ARG A 327 

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8955 (tm-30)
REVERT: A  186 MET cc_start: 0.9191 (ptp) cc_final: 0.8740 (ptp)
REVERT: A  430 MET cc_start: 0.9667 (tpp) cc_final: 0.9421 (mmm)
REVERT: A  784 MET cc_start: 0.9206 (ttm) cc_final: 0.8925 (tmm)
REVERT: A 1034 LEU cc_start: 0.9262 (mp) cc_final: 0.8739 (tt)
REVERT: A 1051 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8203 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9375 (ttp80) cc_final: 0.9143 (ttp80)
  outliers start: 20
  outliers final: 18
  residues processed: 74
  average time/residue: 0.1586
  time to fit residues: 17.8059
Evaluate side-chains
  77 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  789 SER
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0070
   chunk 58 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 88 optimal weight:    0.8980
   chunk 69 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    1.7602

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
A1037 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.074695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.058477 restraints weight = 29819.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 4.04
r_work: 0.2906 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7682  Z= 0.274
  Angle     :  0.544   8.427  10459  Z= 0.280
  Chirality :  0.037   0.191   1206
  Planarity :  0.004   0.042   1315
  Dihedral  :  5.319  75.983   1105
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.72 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.28), residues: 975
  helix:  2.63 (0.21), residues: 628
  sheet: -1.64 (0.63), residues: 64
  loop : -0.66 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 680 
 HIS   0.005   0.001   HIS A 240 
 PHE   0.016   0.001   PHE A 697 
 TYR   0.007   0.001   TYR A 227 
 ARG   0.004   0.000   ARG A 327 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3611.43 seconds
wall clock time: 65 minutes 9.36 seconds (3909.36 seconds total)