Starting phenix.real_space_refine
on Tue Feb  3 23:35:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7upi_26667/02_2026/7upi_26667.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7upi_26667/02_2026/7upi_26667.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7upi_26667/02_2026/7upi_26667.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7upi_26667/02_2026/7upi_26667.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7upi_26667/02_2026/7upi_26667.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7upi_26667/02_2026/7upi_26667.cif"
  }
  resolution = 2.89
  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=   0.000 sd=   0.001
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: 8
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      40      5.16       5
     Cl      1      4.86       5
     C    4937      2.51       5
     N    1324      2.21       5
     O    1467      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7775
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1406
          Classifications: {'peptide': 174}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 165}
    Chain: "B"
      Number of atoms: 2356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2356
          Classifications: {'peptide': 293}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 279}
    Chain: "C"
      Number of atoms: 3977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3977
          Classifications: {'peptide': 505}
          Link IDs: {'PTRANS': 27, 'TRANS': 477}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CL': 1, ' MN': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.58, per 1000 atoms: 0.20
  Number of scatterers: 7775
  At special positions: 0
  Unit cell: (101.46, 92.916, 92.916, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Mn      2     24.99
     Cl      1     17.00
     S      40     16.00
     P       3     15.00
     Mg      1     11.99
     O    1467      8.00
     N    1324      7.00
     C    4937      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 299.9 milliseconds
  

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1844

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      35.9% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 35
    Processing helix  chain 'A' and resid 77 through 84
      removed outlier: 3.560A  pdb=" N   THR A  84 " --> pdb=" O   GLN A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 115
      removed outlier: 3.507A  pdb=" N   PHE A 100 " --> pdb=" O   ASP A  96 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   ASP A 104 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ARG A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 149
    Processing helix  chain 'A' and resid 163 through 178
      removed outlier: 3.950A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 18
    Processing helix  chain 'B' and resid 31 through 48
    Processing helix  chain 'B' and resid 68 through 80
    Processing helix  chain 'B' and resid 99 through 114
    Processing helix  chain 'B' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   ILE B 133 " --> pdb=" O   SER B 129 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY B 135 " --> pdb=" O   ASN B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 144
    Processing helix  chain 'B' and resid 145 through 157
      removed outlier: 3.744A  pdb=" N   TRP B 149 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 188
      removed outlier: 4.019A  pdb=" N   ILE B 186 " --> pdb=" O   SER B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 207
    Processing helix  chain 'B' and resid 228 through 240
    Processing helix  chain 'B' and resid 271 through 275
    Processing helix  chain 'C' and resid 88 through 101
    Processing helix  chain 'C' and resid 116 through 122
    Processing helix  chain 'C' and resid 139 through 145
    Processing helix  chain 'C' and resid 162 through 168
    Processing helix  chain 'C' and resid 185 through 191
      removed outlier: 3.657A  pdb=" N   TYR C 189 " --> pdb=" O   PRO C 185 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG C 190 " --> pdb=" O   SER C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 214
      removed outlier: 3.560A  pdb=" N   LYS C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 237
      removed outlier: 3.534A  pdb=" N   GLY C 235 " --> pdb=" O   ALA C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 260
    Processing helix  chain 'C' and resid 277 through 283
      removed outlier: 3.968A  pdb=" N   GLY C 281 " --> pdb=" O   ASP C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 306
    Processing helix  chain 'C' and resid 325 through 330
    Processing helix  chain 'C' and resid 350 through 355
    Processing helix  chain 'C' and resid 395 through 401
      removed outlier: 4.599A  pdb=" N   GLY C 399 " --> pdb=" O   LEU C 396 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TRP C 401 " --> pdb=" O   PHE C 398 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 418 through 424
      removed outlier: 3.584A  pdb=" N   SER C 422 " --> pdb=" O   GLU C 419 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 447
    Processing helix  chain 'C' and resid 464 through 470
    Processing helix  chain 'C' and resid 487 through 493
      removed outlier: 3.833A  pdb=" N   GLY C 491 " --> pdb=" O   ARG C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 510 through 516
      removed outlier: 3.585A  pdb=" N   GLY C 514 " --> pdb=" O   GLU C 511 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU C 516 " --> pdb=" O   ILE C 513 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 534 through 540
    Processing helix  chain 'C' and resid 557 through 564
      removed outlier: 3.605A  pdb=" N   GLY C 564 " --> pdb=" O   ILE C 560 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 564 through 576
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 56
      removed outlier: 6.572A  pdb=" N   TYR A  14 " --> pdb=" O   ASP A  64 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   LEU A  66 " --> pdb=" O   TYR A  14 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU A  16 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   PHE A  88 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   VAL A 124 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   ILE A  90 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ASN A 126 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   TYR A  92 " --> pdb=" O   ASN A 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 55
      removed outlier: 6.414A  pdb=" N   LEU B  53 " --> pdb=" O   ILE B 164 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   PHE B 170 " --> pdb=" O   CYS B 245 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ILE B 244 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   LEU B 266 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ARG B 246 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 120
      removed outlier: 6.171A  pdb=" N   LYS B  60 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   PHE B 293 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209
      removed outlier: 6.775A  pdb=" N   ASP B 208 " --> pdb=" O   PHE B 227 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 106
      removed outlier: 6.983A  pdb=" N   LEU C 151 " --> pdb=" O   ASP C 175 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LEU C 220 " --> pdb=" O   ASP C 244 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LEU C 243 " --> pdb=" O   ASP C 267 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   LEU C 289 " --> pdb=" O   GLU C 311 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   ASN C 313 " --> pdb=" O   LEU C 289 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   LEU C 312 " --> pdb=" O   THR C 337 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LEU C 336 " --> pdb=" O   ASN C 361 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU C 360 " --> pdb=" O   ASN C 385 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   LEU C 476 " --> pdb=" O   GLY C 500 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   LEU C 499 " --> pdb=" O   TYR C 523 " (cutoff:3.500A)

    261 hydrogen bonds defined for protein.
    597 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: 1.31

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1680
        1.33 -     1.45: 1573
        1.45 -     1.57: 4598
        1.57 -     1.69: 5
        1.69 -     1.81: 59
  Bond restraints: 7915
  Sorted by residual:
  bond pdb=" N   VAL A  39 "
       pdb=" CA  VAL A  39 "
    ideal  model  delta    sigma   weight residual
    1.460  1.487 -0.027 7.30e-03 1.88e+04 1.37e+01
  bond pdb=" N   GLN B 249 "
       pdb=" CA  GLN B 249 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.21e-02 6.83e+03 6.90e+00
  bond pdb=" N   HIS B 248 "
       pdb=" CA  HIS B 248 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.12e+00
  bond pdb=" C   LYS A 127 "
       pdb=" N   VAL A 128 "
    ideal  model  delta    sigma   weight residual
    1.336  1.365 -0.028 1.17e-02 7.31e+03 5.82e+00
  bond pdb=" C2  GTP A 201 "
       pdb=" N3  GTP A 201 "
    ideal  model  delta    sigma   weight residual
    1.380  1.332  0.048 2.00e-02 2.50e+03 5.67e+00
  ... (remaining 7910 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 10634
        2.42 -     4.84: 71
        4.84 -     7.26: 9
        7.26 -     9.69: 6
        9.69 -    12.11: 4
  Bond angle restraints: 10724
  Sorted by residual:
  angle pdb=" PB  GTP A 201 "
        pdb=" O3B GTP A 201 "
        pdb=" PG  GTP A 201 "
      ideal   model   delta    sigma   weight residual
     120.50  132.61  -12.11 3.00e+00 1.11e-01 1.63e+01
  angle pdb=" PA  GTP A 201 "
        pdb=" O3A GTP A 201 "
        pdb=" PB  GTP A 201 "
      ideal   model   delta    sigma   weight residual
     120.50  131.86  -11.36 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" C1' GTP A 201 "
        pdb=" C2' GTP A 201 "
        pdb=" C3' GTP A 201 "
      ideal   model   delta    sigma   weight residual
     111.00   99.71   11.29 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" CA  GLN B  68 "
        pdb=" C   GLN B  68 "
        pdb=" O   GLN B  68 "
      ideal   model   delta    sigma   weight residual
     122.41  118.10    4.31 1.21e+00 6.83e-01 1.27e+01
  angle pdb=" C   TYR B  70 "
        pdb=" CA  TYR B  70 "
        pdb=" CB  TYR B  70 "
      ideal   model   delta    sigma   weight residual
     110.67  117.48   -6.81 1.92e+00 2.71e-01 1.26e+01
  ... (remaining 10719 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.99: 4829
       28.99 -    57.98: 25
       57.98 -    86.97: 1
       86.97 -   115.97: 2
      115.97 -   144.96: 4
  Dihedral angle restraints: 4861
    sinusoidal: 2022
      harmonic: 2839
  Sorted by residual:
  dihedral pdb=" C8  GTP A 201 "
           pdb=" C1' GTP A 201 "
           pdb=" N9  GTP A 201 "
           pdb=" O4' GTP A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -40.36  144.96     1      2.00e+01 2.50e-03 4.36e+01
  dihedral pdb=" O3B GTP A 201 "
           pdb=" O3A GTP A 201 "
           pdb=" PB  GTP A 201 "
           pdb=" PA  GTP A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92   74.77 -143.69     1      2.00e+01 2.50e-03 4.33e+01
  dihedral pdb=" C5' GTP A 201 "
           pdb=" O5' GTP A 201 "
           pdb=" PA  GTP A 201 "
           pdb=" O3A GTP A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -60.23  129.50     1      2.00e+01 2.50e-03 3.93e+01
  ... (remaining 4858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1110
       0.059 -    0.118: 117
       0.118 -    0.177: 8
       0.177 -    0.236: 3
       0.236 -    0.296: 1
  Chirality restraints: 1239
  Sorted by residual:
  chirality pdb=" C3' GTP A 201 "
            pdb=" C2' GTP A 201 "
            pdb=" C4' GTP A 201 "
            pdb=" O3' GTP A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.77    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CB  VAL A 128 "
            pdb=" CA  VAL A 128 "
            pdb=" CG1 VAL A 128 "
            pdb=" CG2 VAL A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  VAL A 128 "
            pdb=" N   VAL A 128 "
            pdb=" C   VAL A 128 "
            pdb=" CB  VAL A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.25    0.19 2.00e-01 2.50e+01 8.75e-01
  ... (remaining 1236 not shown)

  Planarity restraints: 1376
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  70 "   -0.029 2.00e-02 2.50e+03   1.69e-02 5.71e+00
        pdb=" CG  TYR B  70 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  70 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  70 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  70 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  70 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  70 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  70 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  67 "    0.005 2.00e-02 2.50e+03   1.11e-02 1.24e+00
        pdb=" C   GLY B  67 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   GLY B  67 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLN B  68 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B  70 "   -0.005 2.00e-02 2.50e+03   1.10e-02 1.21e+00
        pdb=" C   TYR B  70 "    0.019 2.00e-02 2.50e+03
        pdb=" O   TYR B  70 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASP B  71 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1373 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 16
        2.45 -     3.07: 5117
        3.07 -     3.68: 11252
        3.68 -     4.29: 18278
        4.29 -     4.90: 30404
  Nonbonded interactions: 65067
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 124 "
            pdb="MN    MN B 401 "
     model   vdw
     1.843 2.320
  nonbonded pdb=" OD2 ASP B  92 "
            pdb="MN    MN B 401 "
     model   vdw
     1.934 2.320
  nonbonded pdb=" OG  SER A  27 "
            pdb="MG    MG A 202 "
     model   vdw
     1.984 2.170
  nonbonded pdb=" O2G GTP A 201 "
            pdb="MG    MG A 202 "
     model   vdw
     1.984 2.170
  nonbonded pdb=" NE2 HIS B  66 "
            pdb="MN    MN B 402 "
     model   vdw
     2.052 2.400
  ... (remaining 65062 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.050
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8696
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      :  0.002   0.071   7915  Z= 0.148
  Angle     :  0.547  12.107  10724  Z= 0.271
  Chirality :  0.041   0.296   1239
  Planarity :  0.003   0.027   1376
  Dihedral  :  9.087 144.958   3017
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.12 (0.28), residues: 964
  helix: -0.18 (0.30), residues: 326
  sheet: -0.36 (0.39), residues: 196
  loop :  0.38 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 177 
 TYR   0.036   0.001   TYR B  70 
 PHE   0.005   0.001   PHE B 118 
 TRP   0.003   0.001   TRP B 149 
 HIS   0.003   0.000   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7915)
  covalent geometry    : angle       0.54741 (10724)
  hydrogen bonds       : bond        0.21225 (  261)
  hydrogen bonds       : angle       5.33548 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7958 (mp0) cc_final: 0.7721 (mp0)
REVERT: C  567 PHE cc_start: 0.8644 (m-80) cc_final: 0.8328 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.6148
  time to fit residues: 43.3631
Evaluate side-chains
  42 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.048407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.037489 restraints weight = 27367.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.2596 rms_B_bonded: 3.32
r_work: 0.2431 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   7915  Z= 0.160
  Angle     :  0.506   7.636  10724  Z= 0.259
  Chirality :  0.041   0.131   1239
  Planarity :  0.004   0.069   1376
  Dihedral  :  9.754 148.701   1055
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  4.86 %
    Favored  : 94.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.24 (0.28), residues: 964
  helix: -0.26 (0.31), residues: 336
  sheet: -0.51 (0.38), residues: 196
  loop :  0.37 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 116 
 TYR   0.012   0.001   TYR B  70 
 PHE   0.017   0.001   PHE C 535 
 TRP   0.004   0.001   TRP C 401 
 HIS   0.003   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7915)
  covalent geometry    : angle       0.50603 (10724)
  hydrogen bonds       : bond        0.04322 (  261)
  hydrogen bonds       : angle       4.51671 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9082 (mp0) cc_final: 0.8688 (mp0)
REVERT: C  567 PHE cc_start: 0.9061 (m-80) cc_final: 0.8654 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 45
  average time/residue: 0.4908
  time to fit residues: 23.6405
Evaluate side-chains
  41 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    0.4980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.2936 r_free = 0.2936 target = 0.048476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.037546 restraints weight = 27008.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2600 rms_B_bonded: 3.33
r_work: 0.2440 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7915  Z= 0.104
  Angle     :  0.459   6.715  10724  Z= 0.235
  Chirality :  0.039   0.128   1239
  Planarity :  0.003   0.032   1376
  Dihedral  :  9.404 146.408   1055
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  4.64 %
    Favored  : 94.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.25 (0.28), residues: 964
  helix: -0.24 (0.31), residues: 336
  sheet: -0.63 (0.38), residues: 199
  loop :  0.41 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 116 
 TYR   0.015   0.001   TYR B  70 
 PHE   0.006   0.001   PHE B 118 
 TRP   0.003   0.001   TRP C 401 
 HIS   0.002   0.000   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 7915)
  covalent geometry    : angle       0.45881 (10724)
  hydrogen bonds       : bond        0.03467 (  261)
  hydrogen bonds       : angle       4.31274 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9087 (mp0) cc_final: 0.8596 (mp0)
REVERT: B  290 MET cc_start: 0.9263 (tpp) cc_final: 0.8821 (tpt)
REVERT: C   94 LEU cc_start: 0.9528 (mt) cc_final: 0.9287 (mp)
REVERT: C  362 MET cc_start: 0.8975 (mtm) cc_final: 0.8448 (ptp)
REVERT: C  567 PHE cc_start: 0.9080 (m-80) cc_final: 0.8600 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 45
  average time/residue: 0.5120
  time to fit residues: 24.5344
Evaluate side-chains
  39 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 46 optimal weight:    0.1980
   chunk 63 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0970
   chunk 3 optimal weight:    0.0870
   overall best weight:    0.4760

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

Flipped N/Q/H residues before XYZ refinement:
B 239 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.048629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.037939 restraints weight = 27656.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.2611 rms_B_bonded: 3.33
r_work: 0.2448 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7915  Z= 0.083
  Angle     :  0.445   5.822  10724  Z= 0.229
  Chirality :  0.038   0.128   1239
  Planarity :  0.003   0.032   1376
  Dihedral  :  8.869 145.458   1055
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  4.98 %
    Favored  : 94.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.17 (0.28), residues: 964
  helix: -0.18 (0.31), residues: 330
  sheet: -0.62 (0.38), residues: 199
  loop :  0.46 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 116 
 TYR   0.012   0.001   TYR B  70 
 PHE   0.005   0.001   PHE B 118 
 TRP   0.005   0.001   TRP A  60 
 HIS   0.002   0.000   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 ( 7915)
  covalent geometry    : angle       0.44542 (10724)
  hydrogen bonds       : bond        0.02984 (  261)
  hydrogen bonds       : angle       4.12473 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8655 (tm-30)
REVERT: A   55 GLU cc_start: 0.9184 (tt0) cc_final: 0.8934 (mt-10)
REVERT: C   94 LEU cc_start: 0.9529 (mt) cc_final: 0.9270 (mp)
REVERT: C  362 MET cc_start: 0.8930 (mtm) cc_final: 0.8329 (ptp)
REVERT: C  567 PHE cc_start: 0.9088 (m-80) cc_final: 0.8609 (m-80)
  outliers start: 4
  outliers final: 0
  residues processed: 44
  average time/residue: 0.4896
  time to fit residues: 23.0333
Evaluate side-chains
  39 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 94 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0470
   chunk 63 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    2.3684

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

Flipped N/Q/H residues before XYZ refinement:
C 575 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.045953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2540 r_free = 0.2540 target = 0.035022 restraints weight = 27680.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.2524 rms_B_bonded: 3.33
r_work: 0.2357 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8929
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.027   7915  Z= 0.253
  Angle     :  0.557   7.186  10724  Z= 0.279
  Chirality :  0.042   0.174   1239
  Planarity :  0.004   0.036   1376
  Dihedral  :  8.969 148.247   1055
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  5.43 %
    Favored  : 93.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.30 (0.28), residues: 964
  helix: -0.30 (0.31), residues: 332
  sheet: -0.64 (0.38), residues: 191
  loop :  0.35 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 177 
 TYR   0.017   0.001   TYR B  70 
 PHE   0.009   0.001   PHE A  33 
 TRP   0.006   0.001   TRP C 401 
 HIS   0.005   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 7915)
  covalent geometry    : angle       0.55715 (10724)
  hydrogen bonds       : bond        0.03909 (  261)
  hydrogen bonds       : angle       4.45819 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8772 (tm-30)
REVERT: A   73 GLU cc_start: 0.9337 (mp0) cc_final: 0.8673 (mp0)
REVERT: C   94 LEU cc_start: 0.9589 (mt) cc_final: 0.9378 (mp)
REVERT: C  567 PHE cc_start: 0.9105 (m-80) cc_final: 0.8632 (m-80)
  outliers start: 6
  outliers final: 2
  residues processed: 41
  average time/residue: 0.5708
  time to fit residues: 24.9413
Evaluate side-chains
  39 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue  166 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 67 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.2902 r_free = 0.2902 target = 0.047132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2568 r_free = 0.2568 target = 0.036332 restraints weight = 27483.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2559 rms_B_bonded: 3.37
r_work: 0.2394 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7915  Z= 0.107
  Angle     :  0.477   8.324  10724  Z= 0.243
  Chirality :  0.039   0.144   1239
  Planarity :  0.003   0.035   1376
  Dihedral  :  8.507 145.374   1055
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.77 %
    Favored  : 93.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.27 (0.28), residues: 964
  helix: -0.21 (0.31), residues: 330
  sheet: -0.77 (0.38), residues: 189
  loop :  0.38 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 177 
 TYR   0.013   0.001   TYR B  70 
 PHE   0.007   0.001   PHE A 106 
 TRP   0.003   0.001   TRP A  60 
 HIS   0.004   0.000   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7915)
  covalent geometry    : angle       0.47693 (10724)
  hydrogen bonds       : bond        0.03130 (  261)
  hydrogen bonds       : angle       4.22759 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLU cc_start: 0.9200 (tt0) cc_final: 0.8940 (mt-10)
REVERT: C  362 MET cc_start: 0.9066 (mtm) cc_final: 0.8375 (ptp)
REVERT: C  567 PHE cc_start: 0.9141 (m-80) cc_final: 0.8663 (m-80)
  outliers start: 4
  outliers final: 0
  residues processed: 44
  average time/residue: 0.5402
  time to fit residues: 25.2937
Evaluate side-chains
  38 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 74 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    2.8788

-------------------------------------------------------------------------------
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 = 0.2850 r_free = 0.2850 target = 0.044986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2518 r_free = 0.2518 target = 0.034411 restraints weight = 27701.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.2508 rms_B_bonded: 3.27
r_work: 0.2338 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8945
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.033   7915  Z= 0.309
  Angle     :  0.610   8.862  10724  Z= 0.302
  Chirality :  0.043   0.155   1239
  Planarity :  0.004   0.035   1376
  Dihedral  :  8.797 146.330   1055
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.22 %
    Favored  : 93.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.42 (0.28), residues: 964
  helix: -0.41 (0.31), residues: 332
  sheet: -0.73 (0.38), residues: 191
  loop :  0.30 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 177 
 TYR   0.016   0.001   TYR B  70 
 PHE   0.009   0.001   PHE A 106 
 TRP   0.004   0.001   TRP B 149 
 HIS   0.005   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00696 ( 7915)
  covalent geometry    : angle       0.61014 (10724)
  hydrogen bonds       : bond        0.03930 (  261)
  hydrogen bonds       : angle       4.61082 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9321 (mp0) cc_final: 0.8579 (mp0)
REVERT: C  567 PHE cc_start: 0.9170 (m-80) cc_final: 0.8741 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 39
  average time/residue: 0.4851
  time to fit residues: 20.1665
Evaluate side-chains
  38 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue  166 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.2882 r_free = 0.2882 target = 0.046340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.035582 restraints weight = 27589.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.2539 rms_B_bonded: 3.40
r_work: 0.2373 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8880
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7915  Z= 0.119
  Angle     :  0.518   9.463  10724  Z= 0.261
  Chirality :  0.040   0.139   1239
  Planarity :  0.003   0.035   1376
  Dihedral  :  8.445 144.195   1055
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.56 %
    Favored  : 93.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.41 (0.28), residues: 964
  helix: -0.31 (0.31), residues: 332
  sheet: -0.85 (0.38), residues: 186
  loop :  0.28 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 116 
 TYR   0.013   0.001   TYR B  70 
 PHE   0.007   0.001   PHE A 106 
 TRP   0.003   0.001   TRP A  60 
 HIS   0.004   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7915)
  covalent geometry    : angle       0.51796 (10724)
  hydrogen bonds       : bond        0.03222 (  261)
  hydrogen bonds       : angle       4.36508 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLU cc_start: 0.9218 (tt0) cc_final: 0.8962 (mt-10)
REVERT: C   94 LEU cc_start: 0.9590 (mp) cc_final: 0.9362 (mp)
REVERT: C  362 MET cc_start: 0.9072 (mtm) cc_final: 0.8471 (ptp)
REVERT: C  567 PHE cc_start: 0.9164 (m-80) cc_final: 0.8713 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 42
  average time/residue: 0.5253
  time to fit residues: 23.5898
Evaluate side-chains
  40 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 53 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 47 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.2868 r_free = 0.2868 target = 0.045855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2533 r_free = 0.2533 target = 0.035169 restraints weight = 27778.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.2525 rms_B_bonded: 3.39
r_work: 0.2359 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7915  Z= 0.187
  Angle     :  0.544  10.614  10724  Z= 0.273
  Chirality :  0.041   0.161   1239
  Planarity :  0.003   0.037   1376
  Dihedral  :  8.438 143.562   1055
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  6.67 %
    Favored  : 93.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.43 (0.28), residues: 964
  helix: -0.34 (0.31), residues: 332
  sheet: -0.87 (0.38), residues: 186
  loop :  0.29 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 116 
 TYR   0.014   0.001   TYR B  70 
 PHE   0.007   0.001   PHE A 106 
 TRP   0.004   0.001   TRP B 206 
 HIS   0.005   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 7915)
  covalent geometry    : angle       0.54449 (10724)
  hydrogen bonds       : bond        0.03419 (  261)
  hydrogen bonds       : angle       4.42767 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLU cc_start: 0.9222 (tt0) cc_final: 0.8956 (mt-10)
REVERT: A   73 GLU cc_start: 0.9340 (mp0) cc_final: 0.8508 (mp0)
REVERT: A   79 GLU cc_start: 0.8800 (mp0) cc_final: 0.8577 (pm20)
REVERT: C  173 MET cc_start: 0.9600 (tmm) cc_final: 0.9258 (tmm)
REVERT: C  362 MET cc_start: 0.9155 (mtm) cc_final: 0.8462 (ptp)
REVERT: C  567 PHE cc_start: 0.9174 (m-80) cc_final: 0.8742 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 40
  average time/residue: 0.5755
  time to fit residues: 24.4549
Evaluate side-chains
  39 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.2896 r_free = 0.2896 target = 0.046838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2559 r_free = 0.2559 target = 0.036033 restraints weight = 27484.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.2552 rms_B_bonded: 3.38
r_work: 0.2391 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7915  Z= 0.109
  Angle     :  0.522  11.182  10724  Z= 0.262
  Chirality :  0.040   0.133   1239
  Planarity :  0.003   0.041   1376
  Dihedral  :  8.187 141.291   1055
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.79 %
    Favored  : 93.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.39 (0.28), residues: 964
  helix: -0.31 (0.31), residues: 332
  sheet: -0.88 (0.38), residues: 189
  loop :  0.33 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 116 
 TYR   0.013   0.001   TYR B  70 
 PHE   0.006   0.001   PHE A 106 
 TRP   0.003   0.001   TRP B 206 
 HIS   0.004   0.000   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7915)
  covalent geometry    : angle       0.52204 (10724)
  hydrogen bonds       : bond        0.03042 (  261)
  hydrogen bonds       : angle       4.28792 (  597)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLU cc_start: 0.9222 (tt0) cc_final: 0.8971 (mt-10)
REVERT: A   79 GLU cc_start: 0.8799 (mp0) cc_final: 0.8571 (pm20)
REVERT: C   94 LEU cc_start: 0.9601 (mp) cc_final: 0.9372 (mp)
REVERT: C  173 MET cc_start: 0.9571 (tmm) cc_final: 0.9233 (tmm)
REVERT: C  362 MET cc_start: 0.9045 (mtm) cc_final: 0.8537 (ptp)
REVERT: C  567 PHE cc_start: 0.9170 (m-80) cc_final: 0.8730 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 41
  average time/residue: 0.5912
  time to fit residues: 25.7430
Evaluate side-chains
  40 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0170
   overall best weight:    0.6818

-------------------------------------------------------------------------------
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 = 0.2897 r_free = 0.2897 target = 0.046844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.036161 restraints weight = 27525.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.2560 rms_B_bonded: 3.38
r_work: 0.2401 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7915  Z= 0.101
  Angle     :  0.512  11.395  10724  Z= 0.256
  Chirality :  0.039   0.129   1239
  Planarity :  0.003   0.037   1376
  Dihedral  :  8.049 139.891   1055
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.56 %
    Favored  : 93.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.31 (0.28), residues: 964
  helix: -0.22 (0.31), residues: 330
  sheet: -0.89 (0.37), residues: 194
  loop :  0.40 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 116 
 TYR   0.012   0.001   TYR B  70 
 PHE   0.007   0.001   PHE A 106 
 TRP   0.004   0.000   TRP B 206 
 HIS   0.004   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 7915)
  covalent geometry    : angle       0.51224 (10724)
  hydrogen bonds       : bond        0.02922 (  261)
  hydrogen bonds       : angle       4.21240 (  597)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1570.83 seconds
wall clock time: 27 minutes 37.09 seconds (1657.09 seconds total)