Starting phenix.real_space_refine
on Tue Feb 11 21:38:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7li7_23362/02_2025/7li7_23362.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7li7_23362/02_2025/7li7_23362.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7li7_23362/02_2025/7li7_23362.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7li7_23362/02_2025/7li7_23362.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7li7_23362/02_2025/7li7_23362.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7li7_23362/02_2025/7li7_23362.cif"
  }
  resolution = 4.1
  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=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    4101      2.51       5
     N     960      2.21       5
     O    1082      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6177
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4292
          Classifications: {'peptide': 537}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 514}
    Chain: "B"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 913
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 830
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 114
          Unusual residues: {'CLR': 1, 'D10': 1, 'D12': 3, 'HP6': 5, 'LNK': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
  Time building chain proxies: 4.81, per 1000 atoms: 0.78
  Number of scatterers: 6177
  At special positions: 0
  Unit cell: (71.928, 73.224, 121.176, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1082      8.00
     N     960      7.00
     C    4101      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 112 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 208 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 896.8 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 9 sheets defined
      54.0% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
    Processing helix  chain 'A' and resid 98 through 113
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 114 through 118
      removed outlier: 3.758A  pdb=" N   LEU A 118 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 144
      Proline residue:  A 131  - end of helix
      removed outlier: 3.841A  pdb=" N   GLU A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 154
      removed outlier: 3.849A  pdb=" N   TRP A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.289A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
      removed outlier: 3.615A  pdb=" N   HIS A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 271
    Processing helix  chain 'A' and resid 273 through 282
      removed outlier: 3.730A  pdb=" N   TRP A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 300
      removed outlier: 4.143A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 313
    Processing helix  chain 'A' and resid 325 through 338
    Processing helix  chain 'A' and resid 342 through 349
    Processing helix  chain 'A' and resid 356 through 391
    Processing helix  chain 'A' and resid 403 through 417
      removed outlier: 4.240A  pdb=" N   PHE A 407 " --> pdb=" O   PRO A 403 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 448
      removed outlier: 3.836A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 454
      removed outlier: 3.608A  pdb=" N   GLU A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 461
      removed outlier: 4.125A  pdb=" N   LYS A 460 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 484
      removed outlier: 3.708A  pdb=" N   VAL A 479 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   THR A 480 " --> pdb=" O   GLY A 476 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A 483 " --> pdb=" O   VAL A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 496
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 517 through 530
      removed outlier: 4.456A  pdb=" N   ASP A 524 " --> pdb=" O   GLN A 520 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   GLU A 527 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 541
    Processing helix  chain 'A' and resid 543 through 559
      removed outlier: 3.768A  pdb=" N   ILE A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 585
    Processing helix  chain 'A' and resid 587 through 600
    Processing helix  chain 'A' and resid 603 through 612
    Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25
    Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39
      removed outlier: 3.711A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.559A  pdb=" N   ARG B  69 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.559A  pdb=" N   ARG B  69 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 27
      removed outlier: 3.515A  pdb=" N   ALA C  39 " --> pdb=" O   ILE C  99 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   PHE C  95 " --> pdb=" O   CYS C  43 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR C  94 " --> pdb=" O   SER C  91 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 32
      removed outlier: 6.241A  pdb=" N   LEU C  31 " --> pdb=" O   GLU C 129 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR C 126 " --> pdb=" O   TYR C 110 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR C 110 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE C 111 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 32
      removed outlier: 6.241A  pdb=" N   LEU C  31 " --> pdb=" O   GLU C 129 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR C 126 " --> pdb=" O   TYR C 110 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR C 110 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR C 121 " --> pdb=" O   GLN C 114 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 51
      removed outlier: 3.587A  pdb=" N   ASN C  51 " --> pdb=" O   ILE C  54 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 73

    319 hydrogen bonds defined for protein.
    900 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: 1.89

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1814
        1.34 -     1.46: 1597
        1.46 -     1.58: 2889
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 6349
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.41e+00
  bond pdb=" N   SER C  48 "
       pdb=" CA  SER C  48 "
    ideal  model  delta    sigma   weight residual
    1.458  1.482 -0.024 1.90e-02 2.77e+03 1.64e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.51e+00
  bond pdb=" C   GLU C  47 "
       pdb=" N   SER C  48 "
    ideal  model  delta    sigma   weight residual
    1.329  1.345 -0.016 1.40e-02 5.10e+03 1.35e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.21e+00
  ... (remaining 6344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 8434
        1.88 -     3.75: 125
        3.75 -     5.63: 49
        5.63 -     7.50: 3
        7.50 -     9.38: 1
  Bond angle restraints: 8612
  Sorted by residual:
  angle pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
        pdb=" CA  SER C  48 "
      ideal   model   delta    sigma   weight residual
     121.70  131.08   -9.38 1.80e+00 3.09e-01 2.71e+01
  angle pdb=" N   TRP A 197 "
        pdb=" CA  TRP A 197 "
        pdb=" C   TRP A 197 "
      ideal   model   delta    sigma   weight residual
     114.56  111.00    3.56 1.27e+00 6.20e-01 7.84e+00
  angle pdb=" C13 CLR A 710 "
        pdb=" C17 CLR A 710 "
        pdb=" C20 CLR A 710 "
      ideal   model   delta    sigma   weight residual
     119.60  112.55    7.05 3.00e+00 1.11e-01 5.52e+00
  angle pdb=" C20 CLR A 710 "
        pdb=" C22 CLR A 710 "
        pdb=" C23 CLR A 710 "
      ideal   model   delta    sigma   weight residual
     115.57  108.76    6.81 3.00e+00 1.11e-01 5.16e+00
  angle pdb=" CA  GLU C  47 "
        pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
      ideal   model   delta    sigma   weight residual
     115.49  118.10   -2.61 1.24e+00 6.50e-01 4.42e+00
  ... (remaining 8607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 3379
       17.81 -    35.61: 284
       35.61 -    53.42: 40
       53.42 -    71.23: 5
       71.23 -    89.03: 2
  Dihedral angle restraints: 3710
    sinusoidal: 1510
      harmonic: 2200
  Sorted by residual:
  dihedral pdb=" CB  GLU A 453 "
           pdb=" CG  GLU A 453 "
           pdb=" CD  GLU A 453 "
           pdb=" OE1 GLU A 453 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.03  -89.03     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU A 136 "
           pdb=" CG  GLU A 136 "
           pdb=" CD  GLU A 136 "
           pdb=" OE1 GLU A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.87   84.87     1      3.00e+01 1.11e-03 9.71e+00
  dihedral pdb=" CA  ARG A 596 "
           pdb=" CB  ARG A 596 "
           pdb=" CG  ARG A 596 "
           pdb=" CD  ARG A 596 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.06   57.94     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 3707 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.234: 945
       0.234 -    0.469: 2
       0.469 -    0.703: 0
       0.703 -    0.937: 0
       0.937 -    1.171: 1
  Chirality restraints: 948
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.23   -1.17 2.00e-02 2.50e+03 3.43e+03
  chirality pdb=" C14 CLR A 710 "
            pdb=" C13 CLR A 710 "
            pdb=" C15 CLR A 710 "
            pdb=" C8  CLR A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.67    0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" C9  CLR A 710 "
            pdb=" C10 CLR A 710 "
            pdb=" C11 CLR A 710 "
            pdb=" C8  CLR A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.70    0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 945 not shown)

  Planarity restraints: 1048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 402 "   -0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A 403 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 403 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 403 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 100 "   -0.021 5.00e-02 4.00e+02   3.18e-02 1.62e+00
        pdb=" N   PRO C 101 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO C 101 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 101 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 589 "   -0.016 5.00e-02 4.00e+02   2.41e-02 9.26e-01
        pdb=" N   PRO A 590 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 590 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 590 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1045 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1874
        2.82 -     3.34: 5815
        3.34 -     3.86: 10355
        3.86 -     4.38: 11298
        4.38 -     4.90: 19568
  Nonbonded interactions: 48910
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 110 "
            pdb=" O   VAL A 397 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ASN A 112 "
            pdb=" NZ  LYS A 319 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   THR A 600 "
            pdb=" NE  ARG A 607 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OD1 ASN A 101 "
            pdb=" NE2 GLN A 332 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" O   SER A 190 "
            pdb=" OG  SER A 190 "
     model   vdw
     2.313 3.040
  ... (remaining 48905 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             3.570
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.520
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6461
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   0.031   6349  Z= 0.142
  Angle     :  0.611   9.376   8612  Z= 0.297
  Chirality :  0.056   1.171    948
  Planarity :  0.003   0.034   1047
  Dihedral  : 12.289  89.034   2305
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -2.70 (0.27), residues: 759
  helix: -0.80 (0.24), residues: 370
  sheet: -1.58 (0.54), residues: 81
  loop : -3.08 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 204 
 HIS   0.001   0.000   HIS A 143 
 PHE   0.016   0.001   PHE A 474 
 TYR   0.012   0.001   TYR A 176 
 ARG   0.006   0.000   ARG A 152 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.4133 (mmmt) cc_final: 0.3539 (mmtp)
REVERT: A  260 MET cc_start: 0.6096 (mmm) cc_final: 0.4406 (tmm)
REVERT: A  267 TYR cc_start: 0.7045 (t80) cc_final: 0.6839 (t80)
REVERT: A  456 HIS cc_start: 0.7952 (p-80) cc_final: 0.7737 (p90)
REVERT: A  463 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6779 (mm-30)
REVERT: A  478 LEU cc_start: 0.6966 (tt) cc_final: 0.6669 (tp)
REVERT: A  514 TRP cc_start: 0.6695 (m100) cc_final: 0.6023 (m-10)
REVERT: B   29 GLU cc_start: 0.8859 (mp0) cc_final: 0.8552 (mp0)
REVERT: B   88 THR cc_start: 0.9257 (m) cc_final: 0.8963 (p)
REVERT: B  125 PHE cc_start: 0.8290 (m-80) cc_final: 0.7888 (m-10)
REVERT: C   33 VAL cc_start: 0.8265 (m) cc_final: 0.8057 (p)
REVERT: C   66 GLN cc_start: 0.7811 (mp10) cc_final: 0.7283 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2201
  time to fit residues: 42.9225
Evaluate side-chains
  117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0040
   chunk 30 optimal weight:    0.5980
   chunk 58 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    0.2980
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 ASN
B  58 GLN
B 132 GLN
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.210790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.200894 restraints weight = 7558.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.199555 restraints weight = 12310.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.190668 restraints weight = 12856.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6349  Z= 0.170
  Angle     :  0.535   9.376   8612  Z= 0.277
  Chirality :  0.040   0.178    948
  Planarity :  0.005   0.091   1047
  Dihedral  :  5.769  59.224    995
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.36 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.88 (0.29), residues: 759
  helix: -0.00 (0.26), residues: 370
  sheet: -1.61 (0.53), residues: 90
  loop : -2.73 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 317 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.016   0.001   PHE A 474 
 TYR   0.014   0.001   TYR B  99 
 ARG   0.004   0.001   ARG B  38 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.4736 (mmmt) cc_final: 0.4480 (mmmt)
REVERT: B   32 LYS cc_start: 0.6428 (mmpt) cc_final: 0.6161 (mmmt)
REVERT: B   57 LYS cc_start: 0.8994 (tttm) cc_final: 0.8656 (ttmm)
REVERT: B  109 ASP cc_start: 0.8532 (p0) cc_final: 0.8050 (p0)
REVERT: C  106 ASP cc_start: 0.8062 (m-30) cc_final: 0.7743 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1864
  time to fit residues: 35.4174
Evaluate side-chains
  116 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0370
   chunk 7 optimal weight:    0.0980
   chunk 42 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 6 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 9 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.3458

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.209259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 117)---------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.198603 restraints weight = 7607.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.198080 restraints weight = 13797.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.187620 restraints weight = 12749.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6349  Z= 0.158
  Angle     :  0.527   9.408   8612  Z= 0.271
  Chirality :  0.040   0.152    948
  Planarity :  0.004   0.064   1047
  Dihedral  :  5.704  59.710    995
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.36 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.46 (0.30), residues: 759
  helix:  0.29 (0.26), residues: 372
  sheet: -1.38 (0.53), residues: 98
  loop : -2.50 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 541 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.019   0.001   PHE A 474 
 TYR   0.013   0.001   TYR B  99 
 ARG   0.004   0.000   ARG A 596 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.4878 (mmmt) cc_final: 0.4299 (mmtp)
REVERT: A  456 HIS cc_start: 0.6926 (p90) cc_final: 0.6706 (p90)
REVERT: C   62 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8384 (tt0)
REVERT: C  106 ASP cc_start: 0.7916 (m-30) cc_final: 0.7598 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1940
  time to fit residues: 35.9360
Evaluate side-chains
  113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0970
   chunk 52 optimal weight:    0.4980
   chunk 56 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  61 GLN
C  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.204792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.198118 restraints weight = 7623.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.197171 restraints weight = 9572.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.195703 restraints weight = 10814.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6876
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6349  Z= 0.176
  Angle     :  0.539   9.446   8612  Z= 0.278
  Chirality :  0.041   0.154    948
  Planarity :  0.004   0.054   1047
  Dihedral  :  5.774  59.509    995
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.58 %
    Favored  : 96.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.24 (0.30), residues: 759
  helix:  0.44 (0.27), residues: 374
  sheet: -1.19 (0.54), residues: 95
  loop : -2.40 (0.34), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 541 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.022   0.001   PHE A 474 
 TYR   0.015   0.001   TYR B  99 
 ARG   0.003   0.000   ARG C  38 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.4924 (mmmt) cc_final: 0.4408 (mmtt)
REVERT: A  291 ILE cc_start: 0.8771 (mm) cc_final: 0.8525 (mm)
REVERT: A  456 HIS cc_start: 0.6354 (p90) cc_final: 0.6110 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1861
  time to fit residues: 33.7649
Evaluate side-chains
  106 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 70 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 64 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0040
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 GLN
B 132 GLN
C  62 GLN
** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.202850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.194575 restraints weight = 7413.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.175637 restraints weight = 11568.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.175652 restraints weight = 12227.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6349  Z= 0.187
  Angle     :  0.545   9.503   8612  Z= 0.284
  Chirality :  0.040   0.160    948
  Planarity :  0.004   0.051   1047
  Dihedral  :  5.907  59.732    995
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.80 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.12 (0.30), residues: 759
  helix:  0.53 (0.27), residues: 371
  sheet: -1.05 (0.54), residues: 95
  loop : -2.32 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 541 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.022   0.001   PHE A 474 
 TYR   0.012   0.001   TYR A 142 
 ARG   0.004   0.001   ARG C  38 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5085 (mmmt) cc_final: 0.4594 (mmtt)
REVERT: A  456 HIS cc_start: 0.7027 (p90) cc_final: 0.6733 (p90)
REVERT: B   32 LYS cc_start: 0.6553 (mmpt) cc_final: 0.6327 (mmmt)
  outliers start: 2
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1642
  time to fit residues: 28.6578
Evaluate side-chains
  106 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0570
   chunk 66 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0030
   chunk 52 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.7312

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
A 217 ASN
A 235 HIS
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 GLN
C  62 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.194763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.184500 restraints weight = 7375.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.164885 restraints weight = 11758.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.164246 restraints weight = 13281.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6349  Z= 0.232
  Angle     :  0.589   9.875   8612  Z= 0.308
  Chirality :  0.042   0.177    948
  Planarity :  0.004   0.054   1047
  Dihedral  :  6.129  59.657    995
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.34 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.09 (0.30), residues: 759
  helix:  0.47 (0.27), residues: 367
  sheet: -0.88 (0.53), residues: 100
  loop : -2.20 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 541 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.027   0.002   PHE A 474 
 TYR   0.012   0.001   TYR A 186 
 ARG   0.003   0.000   ARG B  38 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.620 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5362 (mmmt) cc_final: 0.4536 (mmmt)
REVERT: A  456 HIS cc_start: 0.7044 (p90) cc_final: 0.6687 (p90)
REVERT: B   53 MET cc_start: 0.8361 (mmm) cc_final: 0.8066 (mmt)
REVERT: C   62 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8450 (tt0)
  outliers start: 2
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1701
  time to fit residues: 30.8675
Evaluate side-chains
  115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0020
   chunk 27 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 ASN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.195817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.187306 restraints weight = 7503.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.170238 restraints weight = 12286.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.168096 restraints weight = 11623.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6349  Z= 0.223
  Angle     :  0.594   9.798   8612  Z= 0.308
  Chirality :  0.042   0.169    948
  Planarity :  0.004   0.071   1047
  Dihedral  :  6.231  59.431    995
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.40 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.06 (0.30), residues: 759
  helix:  0.50 (0.27), residues: 364
  sheet: -0.79 (0.54), residues: 100
  loop : -2.22 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 541 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.018   0.001   PHE A 556 
 TYR   0.015   0.002   TYR A 142 
 ARG   0.005   0.000   ARG A 298 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A  141 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7210 (pp30)
REVERT: A  201 LYS cc_start: 0.5531 (mmmt) cc_final: 0.4709 (mmmt)
REVERT: A  291 ILE cc_start: 0.8755 (mm) cc_final: 0.8459 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1667
  time to fit residues: 28.9996
Evaluate side-chains
  116 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0270
   chunk 33 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.195066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.187761 restraints weight = 7301.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.187537 restraints weight = 11490.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.167545 restraints weight = 10963.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6349  Z= 0.213
  Angle     :  0.592   9.686   8612  Z= 0.308
  Chirality :  0.042   0.219    948
  Planarity :  0.005   0.073   1047
  Dihedral  :  6.271  59.408    995
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.01 (0.31), residues: 759
  helix:  0.52 (0.27), residues: 365
  sheet: -0.77 (0.54), residues: 100
  loop : -2.17 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.019   0.001   PHE A 556 
 TYR   0.015   0.001   TYR A 107 
 ARG   0.005   0.000   ARG A 390 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5506 (mmmt) cc_final: 0.4651 (mmmt)
REVERT: A  291 ILE cc_start: 0.8749 (mm) cc_final: 0.8499 (mm)
REVERT: A  456 HIS cc_start: 0.6936 (p90) cc_final: 0.6612 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1737
  time to fit residues: 29.2936
Evaluate side-chains
  112 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 57 optimal weight:    0.0040
   chunk 70 optimal weight:    0.0170
   chunk 19 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.4430

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.196079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.186873 restraints weight = 7479.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.168474 restraints weight = 12047.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.167235 restraints weight = 13358.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.3929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6349  Z= 0.189
  Angle     :  0.582   9.678   8612  Z= 0.301
  Chirality :  0.041   0.204    948
  Planarity :  0.004   0.074   1047
  Dihedral  :  6.219  59.510    995
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -0.89 (0.31), residues: 759
  helix:  0.60 (0.27), residues: 365
  sheet: -0.72 (0.55), residues: 95
  loop : -2.06 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 541 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.019   0.001   PHE A 556 
 TYR   0.017   0.001   TYR A 186 
 ARG   0.003   0.000   ARG B  38 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A  197 TRP cc_start: 0.8218 (m-90) cc_final: 0.7974 (m-90)
REVERT: A  201 LYS cc_start: 0.5373 (mmmt) cc_final: 0.4554 (mmmt)
REVERT: A  291 ILE cc_start: 0.8795 (mm) cc_final: 0.8524 (mm)
REVERT: A  456 HIS cc_start: 0.6971 (p90) cc_final: 0.6647 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1686
  time to fit residues: 29.8502
Evaluate side-chains
  114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.193188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.186143 restraints weight = 7557.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.186143 restraints weight = 12275.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.186143 restraints weight = 12274.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6349  Z= 0.251
  Angle     :  0.631   9.650   8612  Z= 0.328
  Chirality :  0.043   0.182    948
  Planarity :  0.005   0.076   1047
  Dihedral  :  6.394  59.257    995
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.01 (0.31), residues: 759
  helix:  0.47 (0.27), residues: 366
  sheet: -0.80 (0.54), residues: 100
  loop : -2.09 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 317 
 HIS   0.004   0.001   HIS A 143 
 PHE   0.023   0.002   PHE A 556 
 TYR   0.039   0.002   TYR A 410 
 ARG   0.005   0.000   ARG B  38 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.676 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5626 (mmmt) cc_final: 0.4778 (mmmt)
REVERT: A  291 ILE cc_start: 0.8918 (mm) cc_final: 0.8683 (mm)
REVERT: A  390 ARG cc_start: 0.6816 (tpt-90) cc_final: 0.5886 (ttm170)
REVERT: A  456 HIS cc_start: 0.6155 (p90) cc_final: 0.5866 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1734
  time to fit residues: 30.1183
Evaluate side-chains
  113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0670
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0970
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0050
   overall best weight:    0.3130

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.196320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.189282 restraints weight = 7554.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.167198 restraints weight = 11296.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.167897 restraints weight = 13762.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6349  Z= 0.174
  Angle     :  0.592   9.656   8612  Z= 0.305
  Chirality :  0.041   0.194    948
  Planarity :  0.004   0.076   1047
  Dihedral  :  6.313  59.580    995
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -0.90 (0.31), residues: 759
  helix:  0.53 (0.27), residues: 367
  sheet: -0.66 (0.56), residues: 95
  loop : -2.00 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP A 317 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.017   0.001   PHE A 556 
 TYR   0.023   0.001   TYR A 410 
 ARG   0.003   0.000   ARG B  59 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2298.38 seconds
wall clock time: 41 minutes 57.41 seconds (2517.41 seconds total)