Starting phenix.real_space_refine
on Thu Mar  6 03:06:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8el7_28223/03_2025/8el7_28223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8el7_28223/03_2025/8el7_28223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8el7_28223/03_2025/8el7_28223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8el7_28223/03_2025/8el7_28223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8el7_28223/03_2025/8el7_28223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8el7_28223/03_2025/8el7_28223.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.198
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       2      5.49       5
     S      27      5.16       5
     C    2921      2.51       5
     N     802      2.21       5
     O     810      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4562
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1134
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 146, 1118
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 139}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 87
      Conformer: "B"
        Number of residues, atoms: 146, 1118
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 139}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 87
          bond proxies already assigned to first conformer: 1130
      Conformer: "C"
        Number of residues, atoms: 146, 1118
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 139}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 87
          bond proxies already assigned to first conformer: 1130
    Chain: "B"
      Number of atoms: 3423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3423
          Classifications: {'peptide': 458}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PTRANS': 15, 'TRANS': 442}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 230
          Unresolved non-hydrogen angles: 282
          Unresolved non-hydrogen dihedrals: 188
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 19, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 171
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.64, per 1000 atoms: 1.24
  Number of scatterers: 4562
  At special positions: 0
  Unit cell: (54.5344, 80.0974, 110.773, 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      27     16.00
     P       2     15.00
     O     810      8.00
     N     802      7.00
     C    2921      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.35
  Conformation dependent library (CDL) restraints added in 897.1 milliseconds
  

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1168

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 1 sheets defined
      67.2% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 251 through 264
      removed outlier: 3.652A  pdb=" N   ALA A 255 " --> pdb=" O   ARG A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 269
      removed outlier: 3.517A  pdb=" N   LEU A 268 " --> pdb=" O   ASN A 265 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG A 269 " --> pdb=" O   ARG A 266 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 265 through 269'
    Processing helix  chain 'A' and resid 279 through 290
      removed outlier: 3.762A  pdb=" N   GLY A 290 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 297
    Processing helix  chain 'A' and resid 298 through 304
    Processing helix  chain 'A' and resid 317 through 337
      removed outlier: 3.720A  pdb=" N   THR A 321 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A 331 " --> pdb=" O   ILE A 327 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ILE A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER A 335 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 376
    Processing helix  chain 'B' and resid 4 through 11
    Processing helix  chain 'B' and resid 14 through 29
      removed outlier: 4.129A  pdb=" N   ILE B  18 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLU B  19 " --> pdb=" O   ALA B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 38
      No H-bonds generated for 'chain 'B' and resid 36 through 38'
    Processing helix  chain 'B' and resid 39 through 56
      removed outlier: 3.512A  pdb=" N   PHE B  51 " --> pdb=" O   CYS B  47 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL B  55 " --> pdb=" O   PHE B  51 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   LYS B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 74
    Processing helix  chain 'B' and resid 85 through 96
      removed outlier: 3.678A  pdb=" N   MET B  89 " --> pdb=" O   THR B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 128
    Processing helix  chain 'B' and resid 129 through 138
      removed outlier: 3.597A  pdb=" N   GLN B 133 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
      removed outlier: 3.837A  pdb=" N   LYS B 143 " --> pdb=" O   ASN B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 175
    Processing helix  chain 'B' and resid 176 through 184
    Processing helix  chain 'B' and resid 187 through 201
      removed outlier: 4.103A  pdb=" N   LEU B 191 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 238
      removed outlier: 3.535A  pdb=" N   ASN B 236 " --> pdb=" O   LYS B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 248
      No H-bonds generated for 'chain 'B' and resid 246 through 248'
    Processing helix  chain 'B' and resid 249 through 264
    Processing helix  chain 'B' and resid 270 through 286
    Processing helix  chain 'B' and resid 287 through 288
      No H-bonds generated for 'chain 'B' and resid 287 through 288'
    Processing helix  chain 'B' and resid 289 through 297
      removed outlier: 4.747A  pdb=" N   ASP B 294 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   VAL B 295 " --> pdb=" O   CYS B 292 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU B 296 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE B 297 " --> pdb=" O   ASP B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 355
      removed outlier: 3.691A  pdb=" N   HIS B 343 " --> pdb=" O   MET B 339 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LYS B 355 " --> pdb=" O   LYS B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 377
      removed outlier: 4.050A  pdb=" N   THR B 364 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      Proline residue:  B 365  - end of helix
      removed outlier: 3.579A  pdb=" N   ALA B 376 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 389
      removed outlier: 3.787A  pdb=" N   ARG B 381 " --> pdb=" O   HIS B 377 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN B 387 " --> pdb=" O   PHE B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 412
    Processing helix  chain 'B' and resid 413 through 415
      No H-bonds generated for 'chain 'B' and resid 413 through 415'
    Processing helix  chain 'B' and resid 417 through 432
      removed outlier: 3.618A  pdb=" N   LYS B 421 " --> pdb=" O   ASP B 417 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU B 428 " --> pdb=" O   ALA B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 443
      removed outlier: 3.639A  pdb=" N   TYR B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 456
    Processing helix  chain 'B' and resid 475 through 482
    Processing helix  chain 'B' and resid 483 through 485
      No H-bonds generated for 'chain 'B' and resid 483 through 485'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 209
      removed outlier: 6.217A  pdb=" N   ILE A 230 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   PHE A 276 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   PHE A 232 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   ASN A 278 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   VAL A 234 " --> pdb=" O   ASN A 278 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   VAL A 273 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   HIS A 348 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LEU A 275 " --> pdb=" O   HIS A 348 " (cutoff:3.500A)

    245 hydrogen bonds defined for protein.
    710 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: 1.03

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 728
        1.31 -     1.44: 1153
        1.44 -     1.56: 2711
        1.56 -     1.68: 2
        1.68 -     1.81: 38
  Bond restraints: 4632
  Sorted by residual:
  bond pdb=" O3P SEP B 468 "
       pdb=" P   SEP B 468 "
    ideal  model  delta    sigma   weight residual
    1.610  1.477  0.133 2.00e-02 2.50e+03 4.44e+01
  bond pdb=" C   ARG A 375 "
       pdb=" CA BARG A 375 "
    ideal  model  delta    sigma   weight residual
    1.522  1.430  0.091 1.40e-02 5.10e+03 4.26e+01
  bond pdb=" C   ARG A 375 "
       pdb=" CA CARG A 375 "
    ideal  model  delta    sigma   weight residual
    1.522  1.430  0.091 1.40e-02 5.10e+03 4.26e+01
  bond pdb=" O1P SEP B 468 "
       pdb=" P   SEP B 468 "
    ideal  model  delta    sigma   weight residual
    1.610  1.480  0.130 2.00e-02 2.50e+03 4.22e+01
  bond pdb=" O2P SEP B 468 "
       pdb=" P   SEP B 468 "
    ideal  model  delta    sigma   weight residual
    1.610  1.481  0.129 2.00e-02 2.50e+03 4.16e+01
  ... (remaining 4627 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 6104
        1.52 -     3.03: 145
        3.03 -     4.55: 33
        4.55 -     6.06: 10
        6.06 -     7.58: 3
  Bond angle restraints: 6295
  Sorted by residual:
  angle pdb=" N   GLU B   4 "
        pdb=" CA  GLU B   4 "
        pdb=" C   GLU B   4 "
      ideal   model   delta    sigma   weight residual
     111.28  115.77   -4.49 1.09e+00 8.42e-01 1.70e+01
  angle pdb=" C   TRP B 466 "
        pdb=" N   TYR B 467 "
        pdb=" CA  TYR B 467 "
      ideal   model   delta    sigma   weight residual
     121.70  114.71    6.99 1.80e+00 3.09e-01 1.51e+01
  angle pdb=" CA  TRP B 466 "
        pdb=" C   TRP B 466 "
        pdb=" N   TYR B 467 "
      ideal   model   delta    sigma   weight residual
     116.02  121.32   -5.30 1.42e+00 4.96e-01 1.39e+01
  angle pdb=" N   ALA B  15 "
        pdb=" CA  ALA B  15 "
        pdb=" C   ALA B  15 "
      ideal   model   delta    sigma   weight residual
     113.38  117.91   -4.53 1.23e+00 6.61e-01 1.35e+01
  angle pdb=" N   GLY B  13 "
        pdb=" CA  GLY B  13 "
        pdb=" C   GLY B  13 "
      ideal   model   delta    sigma   weight residual
     112.73  116.85   -4.12 1.20e+00 6.94e-01 1.18e+01
  ... (remaining 6290 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 2582
       17.32 -    34.64: 188
       34.64 -    51.96: 31
       51.96 -    69.28: 6
       69.28 -    86.60: 5
  Dihedral angle restraints: 2812
    sinusoidal: 1029
      harmonic: 1783
  Sorted by residual:
  dihedral pdb=" CA  GLY B  13 "
           pdb=" C   GLY B  13 "
           pdb=" N   GLU B  14 "
           pdb=" CA  GLU B  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.43  -24.57     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" C   TPO B 473 "
           pdb=" N   TPO B 473 "
           pdb=" CA  TPO B 473 "
           pdb=" CB  TPO B 473 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.38   -9.22     0      2.50e+00 1.60e-01 1.36e+01
  dihedral pdb=" N   TRP B 466 "
           pdb=" C   TRP B 466 "
           pdb=" CA  TRP B 466 "
           pdb=" CB  TRP B 466 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.49    8.31     0      2.50e+00 1.60e-01 1.10e+01
  ... (remaining 2809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 541
       0.038 -    0.077: 177
       0.077 -    0.115: 39
       0.115 -    0.154: 10
       0.154 -    0.192: 4
  Chirality restraints: 771
  Sorted by residual:
  chirality pdb=" CA  ALA B  15 "
            pdb=" N   ALA B  15 "
            pdb=" C   ALA B  15 "
            pdb=" CB  ALA B  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.29    0.19 2.00e-01 2.50e+01 9.25e-01
  chirality pdb=" CA BARG A 375 "
            pdb=" N   ARG A 375 "
            pdb=" C   ARG A 375 "
            pdb=" CB BARG A 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.05e-01
  chirality pdb=" CA CARG A 375 "
            pdb=" N   ARG A 375 "
            pdb=" C   ARG A 375 "
            pdb=" CB CARG A 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.05e-01
  ... (remaining 768 not shown)

  Planarity restraints: 789
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 463 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.92e+00
        pdb=" C   GLY B 463 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   GLY B 463 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASP B 464 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B   5 "    0.007 2.00e-02 2.50e+03   1.37e-02 1.88e+00
        pdb=" C   ARG B   5 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ARG B   5 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ALA B   6 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 478 "   -0.006 2.00e-02 2.50e+03   1.18e-02 1.40e+00
        pdb=" C   TYR B 478 "    0.020 2.00e-02 2.50e+03
        pdb=" O   TYR B 478 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LYS B 479 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 786 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1226
        2.82 -     3.34: 4034
        3.34 -     3.86: 6742
        3.86 -     4.38: 7705
        4.38 -     4.90: 14105
  Nonbonded interactions: 33812
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  80 "
            pdb=" OG1 THR B  84 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   LEU B  70 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" N   GLU B   3 "
            pdb=" OE1 GLU B   3 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" O   PRO B 399 "
            pdb=" ND2 ASN B 407 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" N   ASP B 464 "
            pdb=" OD1 ASP B 464 "
     model   vdw
     2.407 3.120
  ... (remaining 33807 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=0.25 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:             1.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.830
  Find NCS groups from input model:        0.040
  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:12.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
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      :  0.006   0.133   4632  Z= 0.392
  Angle     :  0.611   7.578   6295  Z= 0.356
  Chirality :  0.042   0.192    771
  Planarity :  0.004   0.028    789
  Dihedral  : 13.128  86.604   1644
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.35), residues: 582
  helix:  1.64 (0.28), residues: 355
  sheet:  0.82 (0.97), residues: 32
  loop : -1.30 (0.42), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 466 
 HIS   0.003   0.001   HIS B 262 
 PHE   0.012   0.001   PHE B 163 
 TYR   0.009   0.001   TYR B 334 
 ARG   0.003   0.000   ARG A 328 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B  181 GLN cc_start: 0.7585 (mt0) cc_final: 0.7336 (mt0)
REVERT: B  335 ASN cc_start: 0.7658 (t0) cc_final: 0.7363 (t0)
REVERT: B  372 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6962 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 1.4768
  time to fit residues: 88.7129
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0370
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.9662

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
B 491 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.136384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.097687 restraints weight = 19671.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 4.09
r_work: 0.2936 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4632  Z= 0.161
  Angle     :  0.484   5.754   6295  Z= 0.249
  Chirality :  0.039   0.134    771
  Planarity :  0.004   0.036    789
  Dihedral  :  3.496  12.768    653
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  6.07 %
    Favored  : 92.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.36), residues: 582
  helix:  1.76 (0.28), residues: 368
  sheet:  0.70 (0.96), residues: 32
  loop : -1.31 (0.43), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 466 
 HIS   0.005   0.001   HIS A 343 
 PHE   0.014   0.001   PHE B 163 
 TYR   0.006   0.001   TYR A 344 
 ARG   0.001   0.000   ARG B 381 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.528 
Fit side-chains
REVERT: B  335 ASN cc_start: 0.7853 (t0) cc_final: 0.7489 (t0)
REVERT: B  372 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7210 (mp0)
  outliers start: 6
  outliers final: 2
  residues processed: 45
  average time/residue: 1.4300
  time to fit residues: 66.8177
Evaluate side-chains
  43 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.131172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.099072 restraints weight = 24651.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 4.99
r_work: 0.2741 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2745 r_free = 0.2745    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2745 r_free = 0.2745    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   4632  Z= 0.379
  Angle     :  0.645   6.533   6295  Z= 0.330
  Chirality :  0.045   0.137    771
  Planarity :  0.005   0.039    789
  Dihedral  :  3.966  13.340    653
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  6.51 %
    Favored  : 91.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.35), residues: 582
  helix:  1.43 (0.27), residues: 358
  sheet:  0.46 (0.94), residues: 32
  loop : -1.32 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 263 
 HIS   0.013   0.002   HIS A 343 
 PHE   0.023   0.002   PHE B 163 
 TYR   0.012   0.002   TYR B 334 
 ARG   0.002   0.000   ARG B 352 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A  279 LYS cc_start: 0.7553 (mttt) cc_final: 0.7344 (mttm)
REVERT: A  333 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.5081 (ptp90)
REVERT: B  335 ASN cc_start: 0.8047 (t0) cc_final: 0.7615 (t0)
REVERT: B  372 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7068 (mp0)
  outliers start: 10
  outliers final: 6
  residues processed: 46
  average time/residue: 1.6603
  time to fit residues: 78.8894
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  487 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0870
   chunk 44 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
B 491 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.138780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.102586 restraints weight = 18825.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 3.66
r_work: 0.3029 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4632  Z= 0.133
  Angle     :  0.441   5.050   6295  Z= 0.230
  Chirality :  0.038   0.129    771
  Planarity :  0.004   0.036    789
  Dihedral  :  3.468  13.627    653
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  8.68 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.36), residues: 582
  helix:  2.02 (0.28), residues: 358
  sheet:  0.69 (0.95), residues: 32
  loop : -1.20 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 263 
 HIS   0.008   0.001   HIS B 491 
 PHE   0.013   0.001   PHE B 163 
 TYR   0.006   0.001   TYR B 334 
 ARG   0.001   0.000   ARG A 366 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.585 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.4805 (ptp90)
REVERT: B  150 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.6459 (mtmm)
REVERT: B  335 ASN cc_start: 0.7854 (t0) cc_final: 0.7426 (t0)
REVERT: B  372 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6842 (mp0)
  outliers start: 9
  outliers final: 5
  residues processed: 47
  average time/residue: 1.6632
  time to fit residues: 80.6794
Evaluate side-chains
  45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 20 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.135514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.099278 restraints weight = 19230.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 3.68
r_work: 0.2964 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4632  Z= 0.198
  Angle     :  0.490   5.008   6295  Z= 0.253
  Chirality :  0.040   0.133    771
  Planarity :  0.004   0.037    789
  Dihedral  :  3.526  14.209    653
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 1.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.20 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.36), residues: 582
  helix:  1.99 (0.28), residues: 358
  sheet:  0.68 (0.96), residues: 32
  loop : -1.18 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 263 
 HIS   0.009   0.002   HIS B 491 
 PHE   0.017   0.002   PHE B 163 
 TYR   0.008   0.001   TYR B 334 
 ARG   0.001   0.000   ARG A 366 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.4768 (ptp90)
REVERT: B  335 ASN cc_start: 0.7893 (t0) cc_final: 0.7454 (t0)
REVERT: B  372 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6879 (mp0)
  outliers start: 8
  outliers final: 6
  residues processed: 43
  average time/residue: 1.6650
  time to fit residues: 73.9511
Evaluate side-chains
  45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  487 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0670
   chunk 4 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0050
   chunk 53 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.5132

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

Flipped N/Q/H residues before XYZ refinement:
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.141864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.105078 restraints weight = 20103.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 3.81
r_work: 0.3024 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4632  Z= 0.112
  Angle     :  0.406   5.001   6295  Z= 0.210
  Chirality :  0.037   0.124    771
  Planarity :  0.003   0.034    789
  Dihedral  :  3.235  18.303    653
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.76 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.36), residues: 582
  helix:  2.18 (0.28), residues: 364
  sheet:  0.81 (0.98), residues: 32
  loop : -0.98 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 204 
 HIS   0.008   0.001   HIS B 491 
 PHE   0.014   0.001   PHE A 232 
 TYR   0.005   0.001   TYR B 334 
 ARG   0.001   0.000   ARG B 261 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.678 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.4701 (ptp90)
REVERT: B  150 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.6425 (mtmm)
REVERT: B  335 ASN cc_start: 0.7853 (t0) cc_final: 0.7432 (t0)
REVERT: B  372 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6736 (mp0)
  outliers start: 10
  outliers final: 6
  residues processed: 46
  average time/residue: 1.5746
  time to fit residues: 75.0289
Evaluate side-chains
  45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0070
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    0.2980
   chunk 57 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.5400

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

Flipped N/Q/H residues before XYZ refinement:
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.142690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.105444 restraints weight = 21349.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 4.06
r_work: 0.2927 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   4632  Z= 0.112
  Angle     :  0.401   4.974   6295  Z= 0.207
  Chirality :  0.037   0.129    771
  Planarity :  0.003   0.034    789
  Dihedral  :  3.141  18.421    653
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  9.98 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.36), residues: 582
  helix:  2.48 (0.28), residues: 356
  sheet:  0.86 (0.97), residues: 32
  loop : -0.84 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 263 
 HIS   0.008   0.001   HIS B 491 
 PHE   0.015   0.001   PHE A 232 
 TYR   0.005   0.001   TYR B 334 
 ARG   0.001   0.000   ARG A 366 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.525 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.4673 (ptp90)
REVERT: B  335 ASN cc_start: 0.7877 (t0) cc_final: 0.7471 (t0)
REVERT: B  372 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6798 (mp0)
  outliers start: 9
  outliers final: 5
  residues processed: 44
  average time/residue: 1.6924
  time to fit residues: 76.9482
Evaluate side-chains
  45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.138808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.102124 restraints weight = 17666.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 3.72
r_work: 0.2988 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4632  Z= 0.150
  Angle     :  0.443   5.357   6295  Z= 0.226
  Chirality :  0.038   0.127    771
  Planarity :  0.003   0.035    789
  Dihedral  :  3.264  18.522    653
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.20 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.36), residues: 582
  helix:  2.36 (0.28), residues: 358
  sheet:  0.90 (0.97), residues: 32
  loop : -0.99 (0.44), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 263 
 HIS   0.008   0.001   HIS B 491 
 PHE   0.020   0.001   PHE A 232 
 TYR   0.006   0.001   TYR B 334 
 ARG   0.001   0.000   ARG B 352 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.4617 (ptp90)
REVERT: B  150 LYS cc_start: 0.6998 (mtpp) cc_final: 0.6684 (mtmm)
REVERT: B  335 ASN cc_start: 0.7852 (t0) cc_final: 0.7411 (t0)
REVERT: B  372 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6682 (mp0)
  outliers start: 9
  outliers final: 6
  residues processed: 44
  average time/residue: 1.7755
  time to fit residues: 80.6321
Evaluate side-chains
  45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.141412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.104441 restraints weight = 19878.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 3.91
r_work: 0.2992 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4632  Z= 0.140
  Angle     :  0.433   5.010   6295  Z= 0.221
  Chirality :  0.038   0.127    771
  Planarity :  0.003   0.034    789
  Dihedral  :  3.275  20.625    653
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.20 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.36), residues: 582
  helix:  2.36 (0.28), residues: 358
  sheet:  0.93 (0.97), residues: 32
  loop : -1.00 (0.44), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 263 
 HIS   0.008   0.001   HIS B 491 
 PHE   0.019   0.001   PHE A 232 
 TYR   0.005   0.001   TYR B 334 
 ARG   0.001   0.000   ARG B 352 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.4621 (ptp90)
REVERT: B  150 LYS cc_start: 0.7014 (mtpp) cc_final: 0.6691 (mtmm)
REVERT: B  335 ASN cc_start: 0.7848 (t0) cc_final: 0.7403 (t0)
REVERT: B  372 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6678 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 43
  average time/residue: 1.7400
  time to fit residues: 77.2298
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  487 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 1 optimal weight:    0.0570
   chunk 18 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.1980
   chunk 21 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.6502

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

Flipped N/Q/H residues before XYZ refinement:
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.140124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.104533 restraints weight = 14417.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 3.28
r_work: 0.3058 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4632  Z= 0.122
  Angle     :  0.415   4.986   6295  Z= 0.212
  Chirality :  0.037   0.126    771
  Planarity :  0.003   0.034    789
  Dihedral  :  3.216  21.696    653
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.63 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.36), residues: 582
  helix:  2.50 (0.28), residues: 353
  sheet:  0.95 (0.97), residues: 32
  loop : -0.77 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 263 
 HIS   0.009   0.001   HIS B 491 
 PHE   0.018   0.001   PHE A 232 
 TYR   0.005   0.001   TYR B 334 
 ARG   0.001   0.000   ARG B 179 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.473 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.4651 (ptp90)
REVERT: B  335 ASN cc_start: 0.7840 (t0) cc_final: 0.7411 (t0)
REVERT: B  372 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6759 (mp0)
  outliers start: 8
  outliers final: 6
  residues processed: 43
  average time/residue: 1.7339
  time to fit residues: 76.9193
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  487 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0370
   chunk 55 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 56 optimal weight:    0.1980
   chunk 11 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.0262

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 ASN
B 491 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.138983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.101673 restraints weight = 21469.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 4.05
r_work: 0.2883 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4632  Z= 0.157
  Angle     :  0.441   5.013   6295  Z= 0.227
  Chirality :  0.038   0.128    771
  Planarity :  0.003   0.034    789
  Dihedral  :  3.297  21.624    653
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.85 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.36), residues: 582
  helix:  2.32 (0.28), residues: 358
  sheet:  0.94 (0.97), residues: 32
  loop : -1.01 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 263 
 HIS   0.009   0.001   HIS B 491 
 PHE   0.020   0.001   PHE A 232 
 TYR   0.006   0.001   TYR B 334 
 ARG   0.001   0.000   ARG B 352 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3403.49 seconds
wall clock time: 58 minutes 50.05 seconds (3530.05 seconds total)