Starting phenix.real_space_refine
on Tue Mar  3 18:07:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k0l_22601/03_2026/7k0l_22601.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k0l_22601/03_2026/7k0l_22601.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k0l_22601/03_2026/7k0l_22601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k0l_22601/03_2026/7k0l_22601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k0l_22601/03_2026/7k0l_22601.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k0l_22601/03_2026/7k0l_22601.cif"
  }
  resolution = 3.4
  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=  -0.003 sd=   0.047
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      44      5.16       5
     C    4877      2.51       5
     N    1293      2.21       5
     O    1404      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7619
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3284
          Classifications: {'peptide': 423}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 21, 'TRANS': 401}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 3883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3883
          Classifications: {'peptide': 492}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 17, 'TRANS': 474}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 409
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 43
          Unusual residues: {'PLP': 1, 'VRP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 1.71, per 1000 atoms: 0.22
  Number of scatterers: 7619
  At special positions: 0
  Unit cell: (95.475, 96.48, 115.575, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P       1     15.00
     O    1404      8.00
     N    1293      7.00
     C    4877      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 183.1 milliseconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1778

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      52.3% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 64
    Processing helix  chain 'A' and resid 77 through 81
    Processing helix  chain 'A' and resid 114 through 129
    Processing helix  chain 'A' and resid 142 through 157
      removed outlier: 3.713A  pdb=" N   LEU A 146 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 179
      removed outlier: 3.501A  pdb=" N   THR A 170 " --> pdb=" O   TYR A 166 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ILE A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ILE A 175 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 192 through 202
    Processing helix  chain 'A' and resid 213 through 231
      removed outlier: 3.515A  pdb=" N   LEU A 217 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 288 through 294
    Processing helix  chain 'A' and resid 321 through 326
    Processing helix  chain 'A' and resid 327 through 332
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 342 through 359
    Processing helix  chain 'A' and resid 361 through 378
      removed outlier: 3.660A  pdb=" N   GLN A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 422
    Processing helix  chain 'A' and resid 453 through 472
    Processing helix  chain 'B' and resid 67 through 94
    Processing helix  chain 'B' and resid 105 through 109
    Processing helix  chain 'B' and resid 116 through 126
      removed outlier: 4.704A  pdb=" N   TYR B 122 " --> pdb=" O   PHE B 118 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   THR B 123 " --> pdb=" O   GLU B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 134
      removed outlier: 3.612A  pdb=" N   ARG B 131 " --> pdb=" O   MET B 128 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   ASP B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 200
    Processing helix  chain 'B' and resid 213 through 228
      removed outlier: 3.526A  pdb=" N   GLU B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 250
      Proline residue:  B 247  - end of helix
      removed outlier: 3.570A  pdb=" N   VAL B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 273
    Processing helix  chain 'B' and resid 284 through 299
    Processing helix  chain 'B' and resid 326 through 338
    Processing helix  chain 'B' and resid 358 through 364
    Processing helix  chain 'B' and resid 366 through 370
      removed outlier: 3.614A  pdb=" N   VAL B 370 " --> pdb=" O   PRO B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 402
    Processing helix  chain 'B' and resid 402 through 408
    Processing helix  chain 'B' and resid 412 through 427
    Processing helix  chain 'B' and resid 433 through 457
      removed outlier: 3.865A  pdb=" N   GLU B 437 " --> pdb=" O   SER B 433 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   VAL B 439 " --> pdb=" O   GLY B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 489
      removed outlier: 3.528A  pdb=" N   ILE B 479 " --> pdb=" O   MET B 475 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLY B 480 " --> pdb=" O   PRO B 476 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY B 483 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 536
    Processing helix  chain 'C' and resid 9 through 24
    Processing helix  chain 'C' and resid 25 through 29
    Processing helix  chain 'C' and resid 30 through 56
      removed outlier: 3.542A  pdb=" N   PHE C  55 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 4.060A  pdb=" N   VAL A  94 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ALA A 425 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164
      removed outlier: 3.690A  pdb=" N   LEU A 302 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP A 188 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   GLU A 245 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386
      removed outlier: 4.437A  pdb=" N   THR A 427 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152
      removed outlier: 6.995A  pdb=" N   ILE B 148 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   LYS B 168 " --> pdb=" O   ILE B 148 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   GLU B 150 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ILE B 166 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      removed outlier: 10.291A  pdb=" N   GLN B 152 " --> pdb=" O   GLY B 164 " (cutoff:3.500A)
      removed outlier: 9.404A  pdb=" N   GLY B 164 " --> pdb=" O   GLN B 152 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   GLY B 492 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ILE B 171 " --> pdb=" O   GLY B 492 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235
      removed outlier: 6.681A  pdb=" N   ILE B 310 " --> pdb=" O   TYR B 340 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   TYR B 342 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ILE B 312 " --> pdb=" O   TYR B 342 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   ASP B 344 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   VAL B 314 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASP B 259 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 8.354A  pdb=" N   GLU B 315 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472
      removed outlier: 3.501A  pdb=" N   ARG B 507 " --> pdb=" O   VAL B 496 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   VAL B 494 " --> pdb=" O   ARG B 509 " (cutoff:3.500A)

    398 hydrogen bonds defined for protein.
    1137 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: 1.06

  Time building geometry restraints manager: 0.87 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: 2465
        1.34 -     1.46: 1174
        1.46 -     1.58: 4063
        1.58 -     1.70: 2
        1.70 -     1.82: 71
  Bond restraints: 7775
  Sorted by residual:
  bond pdb=" N   ASN B 120 "
       pdb=" CA  ASN B 120 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.13e+00
  bond pdb=" N   GLU B 119 "
       pdb=" CA  GLU B 119 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.84e+00
  bond pdb=" N   PHE B 121 "
       pdb=" CA  PHE B 121 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.20e-02 6.94e+03 5.71e+00
  bond pdb=" N   PHE B 118 "
       pdb=" CA  PHE B 118 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.25e-02 6.40e+03 5.54e+00
  bond pdb=" C18 VRP B 602 "
       pdb=" C19 VRP B 602 "
    ideal  model  delta    sigma   weight residual
    1.538  1.572 -0.034 2.00e-02 2.50e+03 2.94e+00
  ... (remaining 7770 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 10164
        1.49 -     2.99: 289
        2.99 -     4.48: 41
        4.48 -     5.98: 7
        5.98 -     7.47: 5
  Bond angle restraints: 10506
  Sorted by residual:
  angle pdb=" CB  MET B 285 "
        pdb=" CG  MET B 285 "
        pdb=" SD  MET B 285 "
      ideal   model   delta    sigma   weight residual
     112.70  120.17   -7.47 3.00e+00 1.11e-01 6.21e+00
  angle pdb=" N   ASN B 120 "
        pdb=" CA  ASN B 120 "
        pdb=" C   ASN B 120 "
      ideal   model   delta    sigma   weight residual
     113.16  110.18    2.98 1.24e+00 6.50e-01 5.79e+00
  angle pdb=" C   TYR B 176 "
        pdb=" N   ASN B 177 "
        pdb=" CA  ASN B 177 "
      ideal   model   delta    sigma   weight residual
     121.54  126.08   -4.54 1.91e+00 2.74e-01 5.64e+00
  angle pdb=" CA  CYS A 133 "
        pdb=" C   CYS A 133 "
        pdb=" N   GLY A 134 "
      ideal   model   delta    sigma   weight residual
     115.67  118.55   -2.88 1.23e+00 6.61e-01 5.50e+00
  angle pdb=" CA  GLU B 119 "
        pdb=" C   GLU B 119 "
        pdb=" O   GLU B 119 "
      ideal   model   delta    sigma   weight residual
     120.55  118.10    2.45 1.06e+00 8.90e-01 5.34e+00
  ... (remaining 10501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.52: 4438
       22.52 -    45.03: 236
       45.03 -    67.55: 14
       67.55 -    90.07: 3
       90.07 -   112.58: 1
  Dihedral angle restraints: 4692
    sinusoidal: 1908
      harmonic: 2784
  Sorted by residual:
  dihedral pdb=" C5A PLP B 601 "
           pdb=" O4P PLP B 601 "
           pdb=" P   PLP B 601 "
           pdb=" O1P PLP B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      76.43 -170.99 -112.58     1      2.00e+01 2.50e-03 3.32e+01
  dihedral pdb=" CA  THR B 400 "
           pdb=" C   THR B 400 "
           pdb=" N   HIS B 401 "
           pdb=" CA  HIS B 401 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.35  -15.65     0      5.00e+00 4.00e-02 9.80e+00
  dihedral pdb=" CB  GLU B 197 "
           pdb=" CG  GLU B 197 "
           pdb=" CD  GLU B 197 "
           pdb=" OE1 GLU B 197 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.48  -80.48     1      3.00e+01 1.11e-03 8.90e+00
  ... (remaining 4689 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 884
       0.044 -    0.087: 189
       0.087 -    0.131: 82
       0.131 -    0.174: 3
       0.174 -    0.218: 1
  Chirality restraints: 1159
  Sorted by residual:
  chirality pdb=" C18 VRP B 602 "
            pdb=" C17 VRP B 602 "
            pdb=" C19 VRP B 602 "
            pdb=" O28 VRP B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ASN B 177 "
            pdb=" N   ASN B 177 "
            pdb=" C   ASN B 177 "
            pdb=" CB  ASN B 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.69e-01
  chirality pdb=" CA  ILE A 242 "
            pdb=" N   ILE A 242 "
            pdb=" C   ILE A 242 "
            pdb=" CB  ILE A 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  ... (remaining 1156 not shown)

  Planarity restraints: 1348
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 498 "   -0.040 5.00e-02 4.00e+02   6.10e-02 5.95e+00
        pdb=" N   PRO B 499 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 499 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 499 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 412 "   -0.037 5.00e-02 4.00e+02   5.61e-02 5.03e+00
        pdb=" N   PRO B 413 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B 413 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 413 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 469 "   -0.027 5.00e-02 4.00e+02   4.14e-02 2.74e+00
        pdb=" N   PRO B 470 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 470 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 470 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1345 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 125
        2.69 -     3.24: 7377
        3.24 -     3.80: 11385
        3.80 -     4.35: 14945
        4.35 -     4.90: 26010
  Nonbonded interactions: 59842
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 176 "
            pdb=" O24 VRP B 602 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OD2 ASP B 259 "
            pdb=" OH  TYR B 318 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OG  SER A 401 "
            pdb=" OD2 ASP A 408 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" NE2 HIS B 263 "
            pdb=" O27 VRP B 602 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OG1 THR A 402 "
            pdb=" OD1 ASP A 408 "
     model   vdw
     2.300 3.040
  ... (remaining 59837 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.880
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.550
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
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      :  0.004   0.116   7776  Z= 0.227
  Angle     :  0.601   7.474  10506  Z= 0.360
  Chirality :  0.042   0.218   1159
  Planarity :  0.004   0.061   1348
  Dihedral  : 12.662 112.583   2914
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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 are not related in a simple way.
  whole:  1.09 (0.27), residues: 958
  helix:  1.86 (0.25), residues: 432
  sheet:  0.64 (0.48), residues: 124
  loop : -0.49 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  95 
 TYR   0.023   0.001   TYR A 166 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.011   0.001   TRP A  64 
 HIS   0.003   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 7775)
  covalent geometry    : angle       0.60143 (10506)
  hydrogen bonds       : bond        0.16052 (  398)
  hydrogen bonds       : angle       5.93674 ( 1137)
  Misc. bond           : bond        0.11625 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.341 
Fit side-chains
REVERT: B  472 MET cc_start: 0.8708 (mmm) cc_final: 0.8463 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0880
  time to fit residues: 7.9379
Evaluate side-chains
  56 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 429 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.094052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.081491 restraints weight = 16376.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.29
r_work: 0.3083 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.0789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7776  Z= 0.149
  Angle     :  0.510   6.695  10506  Z= 0.276
  Chirality :  0.042   0.147   1159
  Planarity :  0.004   0.053   1348
  Dihedral  :  5.451  77.723   1098
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  5.23 %
    Favored  : 94.27 %
  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 are not related in a simple way.
  whole:  1.19 (0.27), residues: 958
  helix:  1.95 (0.25), residues: 445
  sheet:  0.57 (0.46), residues: 131
  loop : -0.49 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  95 
 TYR   0.026   0.001   TYR A 166 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.009   0.001   TRP C  32 
 HIS   0.006   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 7775)
  covalent geometry    : angle       0.51013 (10506)
  hydrogen bonds       : bond        0.04929 (  398)
  hydrogen bonds       : angle       4.74901 ( 1137)
  Misc. bond           : bond        0.00043 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.237 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 56
  average time/residue: 0.0854
  time to fit residues: 6.8013
Evaluate side-chains
  58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain C residue   47 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 77 optimal weight:    0.2980
   chunk 74 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.094389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.081814 restraints weight = 16285.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.29
r_work: 0.3087 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7776  Z= 0.136
  Angle     :  0.489   6.626  10506  Z= 0.262
  Chirality :  0.041   0.142   1159
  Planarity :  0.004   0.052   1348
  Dihedral  :  5.112  82.077   1098
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  6.10 %
    Favored  : 93.03 %
  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 are not related in a simple way.
  whole:  1.20 (0.27), residues: 958
  helix:  2.00 (0.25), residues: 445
  sheet:  0.41 (0.45), residues: 131
  loop : -0.49 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 136 
 TYR   0.019   0.001   TYR A 166 
 PHE   0.013   0.001   PHE B 498 
 TRP   0.009   0.001   TRP C  32 
 HIS   0.005   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7775)
  covalent geometry    : angle       0.48850 (10506)
  hydrogen bonds       : bond        0.04368 (  398)
  hydrogen bonds       : angle       4.50740 ( 1137)
  Misc. bond           : bond        0.00005 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.340 
Fit side-chains
REVERT: B  474 TYR cc_start: 0.8945 (m-80) cc_final: 0.8520 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 63
  average time/residue: 0.0808
  time to fit residues: 7.4478
Evaluate side-chains
  61 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain C residue   47 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 46 optimal weight:    8.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.094037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.081509 restraints weight = 16416.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.29
r_work: 0.3085 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7776  Z= 0.141
  Angle     :  0.481   6.651  10506  Z= 0.257
  Chirality :  0.041   0.139   1159
  Planarity :  0.004   0.050   1348
  Dihedral  :  4.903  82.731   1098
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  7.85 %
    Favored  : 91.41 %
  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 are not related in a simple way.
  whole:  1.18 (0.26), residues: 958
  helix:  2.02 (0.25), residues: 445
  sheet:  0.33 (0.44), residues: 129
  loop : -0.51 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  95 
 TYR   0.017   0.001   TYR A 166 
 PHE   0.013   0.001   PHE A 209 
 TRP   0.009   0.001   TRP C  32 
 HIS   0.004   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7775)
  covalent geometry    : angle       0.48101 (10506)
  hydrogen bonds       : bond        0.04222 (  398)
  hydrogen bonds       : angle       4.40966 ( 1137)
  Misc. bond           : bond        0.00001 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 60
  average time/residue: 0.0617
  time to fit residues: 5.5367
Evaluate side-chains
  61 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain C residue   47 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3381 r_free = 0.3381 target = 0.094795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.082155 restraints weight = 16344.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.31
r_work: 0.3097 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7776  Z= 0.120
  Angle     :  0.460   6.624  10506  Z= 0.246
  Chirality :  0.040   0.138   1159
  Planarity :  0.004   0.049   1348
  Dihedral  :  4.607  72.468   1098
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  8.84 %
    Favored  : 89.91 %
  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 are not related in a simple way.
  whole:  1.26 (0.27), residues: 958
  helix:  2.10 (0.25), residues: 445
  sheet:  0.30 (0.44), residues: 129
  loop : -0.47 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 136 
 TYR   0.016   0.001   TYR A 166 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.009   0.001   TRP C  32 
 HIS   0.004   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7775)
  covalent geometry    : angle       0.46001 (10506)
  hydrogen bonds       : bond        0.03884 (  398)
  hydrogen bonds       : angle       4.33346 ( 1137)
  Misc. bond           : bond        0.00005 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8006 (m170)
REVERT: B  487 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8799 (tp)
REVERT: B  505 GLU cc_start: 0.8339 (mp0) cc_final: 0.8036 (mp0)
  outliers start: 10
  outliers final: 6
  residues processed: 64
  average time/residue: 0.0629
  time to fit residues: 6.1089
Evaluate side-chains
  65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain C residue   47 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    0.3980
   chunk 29 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3384 r_free = 0.3384 target = 0.094973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.082287 restraints weight = 16383.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.31
r_work: 0.3099 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7776  Z= 0.120
  Angle     :  0.458   6.618  10506  Z= 0.244
  Chirality :  0.040   0.138   1159
  Planarity :  0.004   0.048   1348
  Dihedral  :  4.416  63.680   1098
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.59 %
    Favored  : 88.92 %
  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 are not related in a simple way.
  whole:  1.26 (0.27), residues: 958
  helix:  2.10 (0.25), residues: 445
  sheet:  0.30 (0.45), residues: 129
  loop : -0.46 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 225 
 TYR   0.014   0.001   TYR A 166 
 PHE   0.012   0.001   PHE A 168 
 TRP   0.009   0.001   TRP C  32 
 HIS   0.003   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7775)
  covalent geometry    : angle       0.45779 (10506)
  hydrogen bonds       : bond        0.03820 (  398)
  hydrogen bonds       : angle       4.29898 ( 1137)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 HIS cc_start: 0.8523 (OUTLIER) cc_final: 0.8012 (m170)
REVERT: A  469 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7519 (mp-120)
REVERT: B  505 GLU cc_start: 0.8311 (mp0) cc_final: 0.7898 (mp0)
  outliers start: 12
  outliers final: 8
  residues processed: 68
  average time/residue: 0.0693
  time to fit residues: 7.1260
Evaluate side-chains
  66 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  469 GLN
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain C residue   47 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0870
   chunk 47 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.3380 r_free = 0.3380 target = 0.094746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.082102 restraints weight = 16216.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.29
r_work: 0.3096 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7776  Z= 0.122
  Angle     :  0.466   6.619  10506  Z= 0.248
  Chirality :  0.041   0.137   1159
  Planarity :  0.004   0.048   1348
  Dihedral  :  4.323  58.688   1098
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.84 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.27), residues: 958
  helix:  2.16 (0.25), residues: 439
  sheet:  0.27 (0.44), residues: 131
  loop : -0.48 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  95 
 TYR   0.014   0.001   TYR C  50 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.008   0.001   TRP C  32 
 HIS   0.004   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7775)
  covalent geometry    : angle       0.46640 (10506)
  hydrogen bonds       : bond        0.03823 (  398)
  hydrogen bonds       : angle       4.33167 ( 1137)
  Misc. bond           : bond        0.00006 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8009 (m170)
REVERT: A  469 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7520 (mp-120)
REVERT: B  505 GLU cc_start: 0.8294 (mp0) cc_final: 0.7950 (mp0)
  outliers start: 12
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0642
  time to fit residues: 6.7220
Evaluate side-chains
  68 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  469 GLN
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain C residue   47 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 57 optimal weight:    0.0270
   chunk 61 optimal weight:    0.0870
   chunk 92 optimal weight:    0.0970
   chunk 39 optimal weight:    0.4980
   chunk 79 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.2214

-------------------------------------------------------------------------------
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 = 0.3431 r_free = 0.3431 target = 0.097763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.085279 restraints weight = 16158.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.28
r_work: 0.3151 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7776  Z= 0.084
  Angle     :  0.431   6.742  10506  Z= 0.230
  Chirality :  0.039   0.147   1159
  Planarity :  0.004   0.047   1348
  Dihedral  :  4.048  52.790   1098
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.09 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.27), residues: 958
  helix:  2.25 (0.25), residues: 444
  sheet:  0.31 (0.44), residues: 129
  loop : -0.33 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 105 
 TYR   0.007   0.001   TYR C  20 
 PHE   0.010   0.001   PHE A 209 
 TRP   0.009   0.001   TRP C  32 
 HIS   0.002   0.000   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00185 ( 7775)
  covalent geometry    : angle       0.43146 (10506)
  hydrogen bonds       : bond        0.02941 (  398)
  hydrogen bonds       : angle       4.23759 ( 1137)
  Misc. bond           : bond        0.00013 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  469 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7422 (mp-120)
REVERT: B   86 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7876 (t80)
REVERT: B  505 GLU cc_start: 0.8278 (mp0) cc_final: 0.7997 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0614
  time to fit residues: 6.9267
Evaluate side-chains
  67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  469 GLN
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  494 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.095072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.082776 restraints weight = 16281.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.27
r_work: 0.3107 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7776  Z= 0.133
  Angle     :  0.474   6.604  10506  Z= 0.252
  Chirality :  0.041   0.144   1159
  Planarity :  0.004   0.047   1348
  Dihedral  :  4.104  46.927   1098
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.59 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.27), residues: 958
  helix:  2.29 (0.25), residues: 439
  sheet:  0.21 (0.44), residues: 131
  loop : -0.39 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 507 
 TYR   0.013   0.001   TYR C  50 
 PHE   0.013   0.001   PHE B 498 
 TRP   0.007   0.001   TRP C  10 
 HIS   0.003   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7775)
  covalent geometry    : angle       0.47371 (10506)
  hydrogen bonds       : bond        0.03854 (  398)
  hydrogen bonds       : angle       4.26452 ( 1137)
  Misc. bond           : bond        0.00003 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 MET cc_start: 0.8741 (mmt) cc_final: 0.8476 (mmp)
REVERT: A  469 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7540 (mp-120)
REVERT: B   86 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7861 (t80)
REVERT: B  505 GLU cc_start: 0.8281 (mp0) cc_final: 0.8025 (mp0)
  outliers start: 8
  outliers final: 6
  residues processed: 63
  average time/residue: 0.0596
  time to fit residues: 5.8323
Evaluate side-chains
  66 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  469 GLN
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  494 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.095081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.082783 restraints weight = 16239.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.28
r_work: 0.3105 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7776  Z= 0.124
  Angle     :  0.469   6.737  10506  Z= 0.249
  Chirality :  0.041   0.143   1159
  Planarity :  0.004   0.046   1348
  Dihedral  :  4.061  43.141   1098
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.21 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.27), residues: 958
  helix:  2.24 (0.25), residues: 439
  sheet:  0.17 (0.44), residues: 131
  loop : -0.43 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 507 
 TYR   0.013   0.001   TYR C  50 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.009   0.001   TRP C  10 
 HIS   0.003   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7775)
  covalent geometry    : angle       0.46851 (10506)
  hydrogen bonds       : bond        0.03739 (  398)
  hydrogen bonds       : angle       4.27299 ( 1137)
  Misc. bond           : bond        0.00006 (    1)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 MET cc_start: 0.8740 (mmt) cc_final: 0.8444 (mmp)
REVERT: A  469 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7517 (mp-120)
REVERT: B   86 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7809 (t80)
REVERT: B  505 GLU cc_start: 0.8312 (mp0) cc_final: 0.8090 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 62
  average time/residue: 0.0585
  time to fit residues: 5.6968
Evaluate side-chains
  65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  469 GLN
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  494 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0470
   chunk 3 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
B 152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.094889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.082502 restraints weight = 16282.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.28
r_work: 0.3100 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7776  Z= 0.126
  Angle     :  0.475   7.647  10506  Z= 0.251
  Chirality :  0.041   0.145   1159
  Planarity :  0.004   0.046   1348
  Dihedral  :  4.044  39.954   1098
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.21 %
    Favored  : 88.54 %
  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 are not related in a simple way.
  whole:  1.31 (0.27), residues: 958
  helix:  2.22 (0.25), residues: 439
  sheet:  0.18 (0.44), residues: 131
  loop : -0.44 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 507 
 TYR   0.014   0.001   TYR C  50 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.010   0.001   TRP C  10 
 HIS   0.003   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7775)
  covalent geometry    : angle       0.47528 (10506)
  hydrogen bonds       : bond        0.03794 (  398)
  hydrogen bonds       : angle       4.26447 ( 1137)
  Misc. bond           : bond        0.00008 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1743.11 seconds
wall clock time: 30 minutes 38.94 seconds (1838.94 seconds total)