Starting phenix.real_space_refine
on Tue Mar  3 13:38:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7etw_31303/03_2026/7etw_31303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7etw_31303/03_2026/7etw_31303.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/7etw_31303/03_2026/7etw_31303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7etw_31303/03_2026/7etw_31303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7etw_31303/03_2026/7etw_31303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7etw_31303/03_2026/7etw_31303.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      20      5.16       5
     C    3204      2.51       5
     N     784      2.21       5
     O     944      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4952
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1525
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 8, 'TRANS': 188}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 3059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 483, 3059
          Classifications: {'peptide': 483}
          Incomplete info: {'truncation_to_alanine': 225}
          Link IDs: {'PTRANS': 25, 'TRANS': 457}
          Chain breaks: 3
          Unresolved chain link angles: 16
          Unresolved non-hydrogen bonds: 852
          Unresolved non-hydrogen angles: 1104
          Unresolved non-hydrogen dihedrals: 724
          Unresolved non-hydrogen chiralities: 83
          Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 18, 'GLN:plan1': 11, 'GLU:plan': 13, 'TRP:plan': 6, 'TYR:plan': 8, 'PHE:plan': 10, 'HIS:plan': 11, 'ASN:plan1': 5}
          Unresolved non-hydrogen planarities: 456
    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: 340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 340
          Unusual residues: {'AJP': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.20, per 1000 atoms: 0.24
  Number of scatterers: 4952
  At special positions: 0
  Unit cell: (85.098, 86.189, 123.283, 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      20     16.00
     O     944      8.00
     N     784      7.00
     C    3204      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
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN B 641 "
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 355.0 milliseconds
  

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1274

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      64.3% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 48
    Processing helix  chain 'A' and resid 61 through 67
    Processing helix  chain 'A' and resid 72 through 95
      removed outlier: 4.008A  pdb=" N   CYS A  76 " --> pdb=" O   TRP A  72 " (cutoff:3.500A)
      Proline residue:  A  89  - end of helix
      removed outlier: 3.812A  pdb=" N   ASP A  92 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 121
      removed outlier: 3.791A  pdb=" N   VAL A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 147
      removed outlier: 3.525A  pdb=" N   LEU A 133 " --> pdb=" O   ASN A 129 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ALA A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 173
      removed outlier: 3.575A  pdb=" N   GLY A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 184
      No H-bonds generated for 'chain 'A' and resid 182 through 184'
    Processing helix  chain 'A' and resid 185 through 191
      removed outlier: 4.007A  pdb=" N   ARG A 189 " --> pdb=" O   PHE A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 212
      removed outlier: 3.584A  pdb=" N   ILE A 195 " --> pdb=" O   TRP A 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 23
      removed outlier: 3.605A  pdb=" N   PHE B  15 " --> pdb=" O   ILE B  11 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA B  23 " --> pdb=" O   GLY B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 41
      removed outlier: 3.811A  pdb=" N   ILE B  29 " --> pdb=" O   TYR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 131
      removed outlier: 3.626A  pdb=" N   SER B 117 " --> pdb=" O   ASP B 113 " (cutoff:3.500A)
      Proline residue:  B 118  - end of helix
      removed outlier: 3.951A  pdb=" N   GLN B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASN B 131 " --> pdb=" O   GLU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 146
      removed outlier: 3.501A  pdb=" N   GLU B 145 " --> pdb=" O   SER B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 161
      removed outlier: 3.705A  pdb=" N   ARG B 158 " --> pdb=" O   PRO B 155 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   LYS B 159 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 179
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 191 through 197
    Processing helix  chain 'B' and resid 209 through 215
    Processing helix  chain 'B' and resid 244 through 259
      removed outlier: 3.605A  pdb=" N   LEU B 248 " --> pdb=" O   HIS B 244 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   SER B 250 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU B 257 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 284
      No H-bonds generated for 'chain 'B' and resid 282 through 284'
    Processing helix  chain 'B' and resid 285 through 305
      removed outlier: 3.716A  pdb=" N   VAL B 289 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LYS B 305 " --> pdb=" O   PHE B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 336
      removed outlier: 4.364A  pdb=" N   ALA B 316 " --> pdb=" O   LYS B 312 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ALA B 319 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 356
      removed outlier: 3.598A  pdb=" N   LEU B 352 " --> pdb=" O   ILE B 348 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL B 353 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 370
      removed outlier: 5.421A  pdb=" N   LEU B 364 " --> pdb=" O   ASN B 360 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   SER B 367 " --> pdb=" O   VAL B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 409
      removed outlier: 3.854A  pdb=" N   ARG B 380 " --> pdb=" O   GLU B 376 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER B 386 " --> pdb=" O   ALA B 382 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER B 387 " --> pdb=" O   GLN B 383 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   TRP B 390 " --> pdb=" O   SER B 386 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   SER B 391 " --> pdb=" O   SER B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 433
      removed outlier: 4.607A  pdb=" N   LEU B 419 " --> pdb=" O   GLN B 415 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE B 420 " --> pdb=" O   GLU B 416 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   MET B 433 " --> pdb=" O   PHE B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 450
      removed outlier: 3.719A  pdb=" N   THR B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 533
    Processing helix  chain 'B' and resid 534 through 538
    Processing helix  chain 'B' and resid 632 through 639
      removed outlier: 3.996A  pdb=" N   LEU B 636 " --> pdb=" O   HIS B 632 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   PHE B 637 " --> pdb=" O   TRP B 633 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 171 through 172
      removed outlier: 3.805A  pdb=" N   VAL B 232 " --> pdb=" O   SER B 100 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL B  98 " --> pdb=" O   TYR B 234 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   VAL B 654 " --> pdb=" O   GLN B  95 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE B  97 " --> pdb=" O   VAL B 654 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 171 through 172
      removed outlier: 3.805A  pdb=" N   VAL B 232 " --> pdb=" O   SER B 100 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL B  98 " --> pdb=" O   TYR B 234 " (cutoff:3.500A)
      removed outlier: 8.364A  pdb=" N   THR B 658 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LYS B  99 " --> pdb=" O   THR B 658 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 136
      removed outlier: 3.882A  pdb=" N   LEU B 134 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 275
      removed outlier: 4.460A  pdb=" N   VAL B 272 " --> pdb=" O   LEU B 651 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU B 651 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)

    295 hydrogen bonds defined for protein.
    852 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: 0.83

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 747
        1.32 -     1.44: 1388
        1.44 -     1.56: 2907
        1.56 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 5072
  Sorted by residual:
  bond pdb=" C   LYS B 277 "
       pdb=" O   LYS B 277 "
    ideal  model  delta    sigma   weight residual
    1.235  1.281 -0.047 1.18e-02 7.18e+03 1.57e+01
  bond pdb=" N   ARG B 660 "
       pdb=" CA  ARG B 660 "
    ideal  model  delta    sigma   weight residual
    1.458  1.504 -0.046 1.18e-02 7.18e+03 1.55e+01
  bond pdb=" N   VAL B 654 "
       pdb=" CA  VAL B 654 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.043 1.14e-02 7.69e+03 1.45e+01
  bond pdb=" N   VAL B 657 "
       pdb=" CA  VAL B 657 "
    ideal  model  delta    sigma   weight residual
    1.455  1.498 -0.043 1.18e-02 7.18e+03 1.32e+01
  bond pdb=" N   LYS B  99 "
       pdb=" CA  LYS B  99 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.045 1.24e-02 6.50e+03 1.30e+01
  ... (remaining 5067 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 6455
        2.09 -     4.18: 479
        4.18 -     6.27: 73
        6.27 -     8.36: 12
        8.36 -    10.45: 5
  Bond angle restraints: 7024
  Sorted by residual:
  angle pdb=" N   PRO B 104 "
        pdb=" CA  PRO B 104 "
        pdb=" C   PRO B 104 "
      ideal   model   delta    sigma   weight residual
     113.84  104.13    9.71 1.30e+00 5.92e-01 5.58e+01
  angle pdb=" N   ILE A  51 "
        pdb=" CA  ILE A  51 "
        pdb=" C   ILE A  51 "
      ideal   model   delta    sigma   weight residual
     106.32  116.68  -10.36 1.61e+00 3.86e-01 4.14e+01
  angle pdb=" CA  SER B 173 "
        pdb=" C   SER B 173 "
        pdb=" N   PRO B 174 "
      ideal   model   delta    sigma   weight residual
     117.95  122.09   -4.14 7.70e-01 1.69e+00 2.90e+01
  angle pdb=" C   ARG B 267 "
        pdb=" CA  ARG B 267 "
        pdb=" CB  ARG B 267 "
      ideal   model   delta    sigma   weight residual
     116.54  111.29    5.25 1.15e+00 7.56e-01 2.08e+01
  angle pdb=" C   PRO B  89 "
        pdb=" N   VAL B  90 "
        pdb=" CA  VAL B  90 "
      ideal   model   delta    sigma   weight residual
     122.48  128.15   -5.67 1.25e+00 6.40e-01 2.05e+01
  ... (remaining 7019 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.75: 3423
       22.75 -    45.51: 171
       45.51 -    68.26: 26
       68.26 -    91.02: 6
       91.02 -   113.77: 2
  Dihedral angle restraints: 3628
    sinusoidal: 1663
      harmonic: 1965
  Sorted by residual:
  dihedral pdb=" C   ILE A  51 "
           pdb=" N   ILE A  51 "
           pdb=" CA  ILE A  51 "
           pdb=" CB  ILE A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.18   11.18     0      2.50e+00 1.60e-01 2.00e+01
  dihedral pdb=" CA  LYS A 102 "
           pdb=" C   LYS A 102 "
           pdb=" N   ARG A 103 "
           pdb=" CA  ARG A 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.97  -22.03     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  VAL A  55 "
           pdb=" C   VAL A  55 "
           pdb=" N   THR A  56 "
           pdb=" CA  THR A  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.05  -19.95     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 3625 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.254: 958
       0.254 -    0.509: 5
       0.509 -    0.763: 0
       0.763 -    1.018: 0
       1.018 -    1.272: 1
  Chirality restraints: 964
  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   -1.13   -1.27 2.00e-02 2.50e+03 4.04e+03
  chirality pdb=" CA  ILE A  51 "
            pdb=" N   ILE A  51 "
            pdb=" C   ILE A  51 "
            pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.07    0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" C11 AJP A 302 "
            pdb=" C10 AJP A 302 "
            pdb=" C12 AJP A 302 "
            pdb=" C16 AJP A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.47   -0.27 2.00e-01 2.50e+01 1.81e+00
  ... (remaining 961 not shown)

  Planarity restraints: 813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.157 2.00e-02 2.50e+03   1.35e-01 2.27e+02
        pdb=" C7  NAG D   2 "    0.035 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.029 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.219 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.126 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 641 "    0.093 2.00e-02 2.50e+03   1.35e-01 2.26e+02
        pdb=" CG  ASN B 641 "   -0.041 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 641 "    0.039 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 641 "   -0.238 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "    0.148 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.113 2.00e-02 2.50e+03   9.24e-02 1.07e+02
        pdb=" C7  NAG D   1 "    0.030 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.084 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.147 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.020 2.00e-02 2.50e+03
  ... (remaining 810 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 29
        2.45 -     3.07: 4058
        3.07 -     3.68: 6953
        3.68 -     4.29: 9646
        4.29 -     4.90: 14668
  Nonbonded interactions: 35354
  Sorted by model distance:
  nonbonded pdb=" O53 AJP A 302 "
            pdb=" O76 AJP A 302 "
     model   vdw
     1.843 3.040
  nonbonded pdb=" O43 AJP A 304 "
            pdb=" O50 AJP A 304 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" O60 AJP A 303 "
            pdb=" O77 AJP A 303 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   ILE B 280 "
            pdb=" O   GLY B 281 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   ALA B 382 "
            pdb=" OG  SER B 386 "
     model   vdw
     2.268 3.040
  ... (remaining 35349 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:                  0.000
  Normalize map: mean=0, sd=1:             0.270
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.960
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
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      :  0.009   0.130   5074  Z= 0.562
  Angle     :  1.271  26.896   7030  Z= 0.694
  Chirality :  0.076   1.272    964
  Planarity :  0.008   0.135    812
  Dihedral  : 13.698 113.769   2354
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  1.94 %
    Allowed  : 11.64 %
    Favored  : 86.42 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  4.90 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.46 (0.24), residues: 670
  helix: -3.25 (0.19), residues: 375
  sheet: -1.07 (1.06), residues: 26
  loop : -4.37 (0.28), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 631 
 TYR   0.027   0.002   TYR A  88 
 PHE   0.013   0.002   PHE A 155 
 TRP   0.016   0.002   TRP B 633 
 HIS   0.024   0.004   HIS B 632 

Details of bonding type rmsd
  covalent geometry    : bond        0.00926 ( 5072)
  covalent geometry    : angle       1.20659 ( 7024)
  hydrogen bonds       : bond        0.19711 (  289)
  hydrogen bonds       : angle       7.91686 (  852)
  link_BETA1-4         : bond        0.05138 (    1)
  link_BETA1-4         : angle      10.47834 (    3)
  link_NAG-ASN         : bond        0.12959 (    1)
  link_NAG-ASN         : angle      16.28184 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 157
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7211 (ptp-170)
REVERT: A   93 ARG cc_start: 0.7952 (ttt90) cc_final: 0.6894 (tmt170)
REVERT: A  167 VAL cc_start: 0.9082 (t) cc_final: 0.8823 (p)
REVERT: A  208 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8095 (mtt180)
REVERT: A  209 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7534 (tp-100)
REVERT: B  359 GLU cc_start: 0.7777 (mp0) cc_final: 0.7517 (mp0)
REVERT: B  378 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8018 (ttmm)
REVERT: B  383 GLN cc_start: 0.9147 (tt0) cc_final: 0.8482 (mt0)
REVERT: B  388 GLU cc_start: 0.8434 (tp30) cc_final: 0.7912 (tp30)
REVERT: B  442 ILE cc_start: 0.8824 (tp) cc_final: 0.8533 (mm)
REVERT: B  445 ARG cc_start: 0.8511 (ttt90) cc_final: 0.8016 (mmm160)
REVERT: B  447 MET cc_start: 0.7903 (ttt) cc_final: 0.7536 (ttm)
REVERT: B  626 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7315 (mmp80)
REVERT: B  627 LYS cc_start: 0.7899 (mttt) cc_final: 0.7562 (pttm)
REVERT: B  641 ASN cc_start: 0.6111 (t0) cc_final: 0.5609 (t0)
  outliers start: 5
  outliers final: 1
  residues processed: 160
  average time/residue: 0.0853
  time to fit residues: 16.7659
Evaluate side-chains
  106 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:   20.0000
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 120 HIS
A 132 GLN
B  17 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.155756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.130617 restraints weight = 12890.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.133992 restraints weight = 6821.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.136157 restraints weight = 4542.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.137376 restraints weight = 3501.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.138416 restraints weight = 2990.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5074  Z= 0.169
  Angle     :  0.832   8.032   7030  Z= 0.393
  Chirality :  0.046   0.354    964
  Planarity :  0.005   0.083    812
  Dihedral  :  9.491  76.774   1629
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.01 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  7.36 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.30), residues: 670
  helix: -0.97 (0.25), residues: 388
  sheet: -1.08 (0.86), residues: 37
  loop : -3.28 (0.35), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 380 
 TYR   0.030   0.003   TYR A 180 
 PHE   0.021   0.002   PHE B 301 
 TRP   0.017   0.001   TRP A 146 
 HIS   0.012   0.003   HIS B 632 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5072)
  covalent geometry    : angle       0.81988 ( 7024)
  hydrogen bonds       : bond        0.05735 (  289)
  hydrogen bonds       : angle       4.91441 (  852)
  link_BETA1-4         : bond        0.00120 (    1)
  link_BETA1-4         : angle       2.06282 (    3)
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       6.60999 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7610 (tp-100)
REVERT: B  298 TYR cc_start: 0.8464 (t80) cc_final: 0.7302 (t80)
REVERT: B  347 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7425 (mt-10)
REVERT: B  378 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8110 (ttmm)
REVERT: B  383 GLN cc_start: 0.9013 (tt0) cc_final: 0.8451 (mt0)
REVERT: B  442 ILE cc_start: 0.8687 (tp) cc_final: 0.8425 (mm)
REVERT: B  445 ARG cc_start: 0.8431 (ttt90) cc_final: 0.7941 (mmm160)
REVERT: B  626 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7403 (mmp80)
REVERT: B  627 LYS cc_start: 0.7677 (mttt) cc_final: 0.7460 (pttm)
  outliers start: 1
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0823
  time to fit residues: 14.4875
Evaluate side-chains
  107 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 34 optimal weight:   20.0000
   chunk 59 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0010
   chunk 3 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0470
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.4484

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 120 HIS
B 632 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.157719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130383 restraints weight = 12666.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.133830 restraints weight = 6949.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.136042 restraints weight = 4719.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.137352 restraints weight = 3716.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.137731 restraints weight = 3188.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5074  Z= 0.135
  Angle     :  0.717   8.628   7030  Z= 0.340
  Chirality :  0.043   0.309    964
  Planarity :  0.004   0.040    812
  Dihedral  :  8.197  65.580   1629
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.37 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.32), residues: 670
  helix:  0.25 (0.26), residues: 387
  sheet: -0.64 (0.89), residues: 37
  loop : -2.79 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  31 
 TYR   0.009   0.001   TYR B 639 
 PHE   0.025   0.002   PHE B 420 
 TRP   0.016   0.001   TRP A 146 
 HIS   0.020   0.004   HIS B 632 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 5072)
  covalent geometry    : angle       0.70590 ( 7024)
  hydrogen bonds       : bond        0.04695 (  289)
  hydrogen bonds       : angle       4.15664 (  852)
  link_BETA1-4         : bond        0.00506 (    1)
  link_BETA1-4         : angle       2.11081 (    3)
  link_NAG-ASN         : bond        0.00758 (    1)
  link_NAG-ASN         : angle       5.75316 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8196 (t0) cc_final: 0.7325 (t0)
REVERT: A  166 THR cc_start: 0.9076 (m) cc_final: 0.8535 (m)
REVERT: A  170 GLN cc_start: 0.8401 (pm20) cc_final: 0.7807 (pm20)
REVERT: A  209 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7787 (tp-100)
REVERT: B   40 CYS cc_start: 0.6163 (m) cc_final: 0.5926 (m)
REVERT: B  298 TYR cc_start: 0.8521 (t80) cc_final: 0.8124 (t80)
REVERT: B  304 ARG cc_start: 0.8016 (mmm160) cc_final: 0.7736 (tpt90)
REVERT: B  329 MET cc_start: 0.8030 (mtp) cc_final: 0.7806 (mtm)
REVERT: B  378 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8139 (ttmm)
REVERT: B  383 GLN cc_start: 0.8996 (tt0) cc_final: 0.8588 (mt0)
REVERT: B  442 ILE cc_start: 0.8776 (tp) cc_final: 0.8491 (mm)
REVERT: B  445 ARG cc_start: 0.8292 (ttt90) cc_final: 0.7684 (mmm160)
REVERT: B  626 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7398 (mmp80)
REVERT: B  630 PHE cc_start: 0.7762 (t80) cc_final: 0.7330 (m-80)
REVERT: B  641 ASN cc_start: 0.5096 (t0) cc_final: 0.4851 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0796
  time to fit residues: 12.6967
Evaluate side-chains
  107 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 66 optimal weight:   50.0000
   chunk 23 optimal weight:    0.0060
   chunk 56 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 34 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   overall best weight:    1.6002

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 ASN
A 120 HIS
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.152609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.126894 restraints weight = 12788.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.130202 restraints weight = 7036.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.132287 restraints weight = 4828.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.133529 restraints weight = 3775.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.133938 restraints weight = 3231.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   5074  Z= 0.164
  Angle     :  0.713   7.089   7030  Z= 0.338
  Chirality :  0.043   0.331    964
  Planarity :  0.004   0.056    812
  Dihedral  :  7.880  63.467   1629
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  6.12 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.33), residues: 670
  helix:  0.53 (0.26), residues: 391
  sheet:  1.70 (1.15), residues: 22
  loop : -2.84 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  31 
 TYR   0.036   0.002   TYR A  88 
 PHE   0.015   0.002   PHE B 435 
 TRP   0.017   0.001   TRP A 146 
 HIS   0.005   0.001   HIS B 632 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5072)
  covalent geometry    : angle       0.70332 ( 7024)
  hydrogen bonds       : bond        0.04463 (  289)
  hydrogen bonds       : angle       4.03996 (  852)
  link_BETA1-4         : bond        0.00506 (    1)
  link_BETA1-4         : angle       2.17375 (    3)
  link_NAG-ASN         : bond        0.00896 (    1)
  link_NAG-ASN         : angle       5.19756 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.6163 (mm-40) cc_final: 0.5818 (mm-40)
REVERT: A  209 GLN cc_start: 0.8478 (tp-100) cc_final: 0.7843 (tp-100)
REVERT: B   16 TYR cc_start: 0.8183 (t80) cc_final: 0.7657 (t80)
REVERT: B  298 TYR cc_start: 0.8946 (t80) cc_final: 0.8637 (t80)
REVERT: B  378 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8147 (ttmm)
REVERT: B  383 GLN cc_start: 0.9038 (tt0) cc_final: 0.8682 (mt0)
REVERT: B  396 MET cc_start: 0.7628 (ttm) cc_final: 0.7369 (ttm)
REVERT: B  442 ILE cc_start: 0.8793 (tp) cc_final: 0.8543 (mm)
REVERT: B  445 ARG cc_start: 0.8299 (ttt90) cc_final: 0.8096 (ttt-90)
REVERT: B  641 ASN cc_start: 0.5230 (t0) cc_final: 0.4989 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0725
  time to fit residues: 11.8227
Evaluate side-chains
  107 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0770
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 ASN
A 120 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.152302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.124996 restraints weight = 12809.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.128436 restraints weight = 6930.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.130602 restraints weight = 4760.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.131788 restraints weight = 3737.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.132897 restraints weight = 3237.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5074  Z= 0.124
  Angle     :  0.674   9.388   7030  Z= 0.319
  Chirality :  0.042   0.307    964
  Planarity :  0.004   0.041    812
  Dihedral  :  7.567  61.677   1629
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.22 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.33), residues: 670
  helix:  0.78 (0.26), residues: 394
  sheet: -0.32 (0.93), residues: 37
  loop : -2.58 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 208 
 TYR   0.007   0.001   TYR A 178 
 PHE   0.015   0.001   PHE B 435 
 TRP   0.015   0.001   TRP A 146 
 HIS   0.007   0.002   HIS B 632 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5072)
  covalent geometry    : angle       0.66621 ( 7024)
  hydrogen bonds       : bond        0.04062 (  289)
  hydrogen bonds       : angle       3.85722 (  852)
  link_BETA1-4         : bond        0.00301 (    1)
  link_BETA1-4         : angle       2.14237 (    3)
  link_NAG-ASN         : bond        0.00783 (    1)
  link_NAG-ASN         : angle       4.72196 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LEU cc_start: 0.9259 (mp) cc_final: 0.9003 (mt)
REVERT: A   92 ASP cc_start: 0.7921 (t0) cc_final: 0.7674 (t0)
REVERT: A  132 GLN cc_start: 0.6180 (mm-40) cc_final: 0.5710 (mm-40)
REVERT: A  209 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8058 (tp-100)
REVERT: B   16 TYR cc_start: 0.8229 (t80) cc_final: 0.7647 (t80)
REVERT: B  298 TYR cc_start: 0.8928 (t80) cc_final: 0.8557 (t80)
REVERT: B  359 GLU cc_start: 0.7703 (mp0) cc_final: 0.7479 (mp0)
REVERT: B  378 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8226 (ttmm)
REVERT: B  383 GLN cc_start: 0.9046 (tt0) cc_final: 0.8745 (mt0)
REVERT: B  388 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8243 (mm-30)
REVERT: B  442 ILE cc_start: 0.8830 (tp) cc_final: 0.8574 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0693
  time to fit residues: 11.8730
Evaluate side-chains
  106 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0170
   chunk 57 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0470
   chunk 36 optimal weight:    8.9990
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 120 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.155550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.129884 restraints weight = 13263.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.133321 restraints weight = 7167.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.135184 restraints weight = 4853.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.136760 restraints weight = 3848.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.137407 restraints weight = 3234.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.4819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5074  Z= 0.120
  Angle     :  0.653   6.515   7030  Z= 0.309
  Chirality :  0.041   0.299    964
  Planarity :  0.004   0.041    812
  Dihedral  :  7.310  60.032   1629
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.22 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.34), residues: 670
  helix:  0.95 (0.27), residues: 393
  sheet: -0.20 (0.94), residues: 37
  loop : -2.54 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  31 
 TYR   0.026   0.001   TYR A  88 
 PHE   0.015   0.001   PHE B 301 
 TRP   0.015   0.001   TRP A 146 
 HIS   0.009   0.002   HIS B 632 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 5072)
  covalent geometry    : angle       0.64542 ( 7024)
  hydrogen bonds       : bond        0.03957 (  289)
  hydrogen bonds       : angle       3.77267 (  852)
  link_BETA1-4         : bond        0.00320 (    1)
  link_BETA1-4         : angle       2.07442 (    3)
  link_NAG-ASN         : bond        0.00720 (    1)
  link_NAG-ASN         : angle       4.40542 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LEU cc_start: 0.9257 (mp) cc_final: 0.9044 (mt)
REVERT: A  120 HIS cc_start: 0.8451 (t-90) cc_final: 0.8194 (t-170)
REVERT: A  132 GLN cc_start: 0.5932 (mm-40) cc_final: 0.5482 (mm-40)
REVERT: A  203 MET cc_start: 0.9065 (mtp) cc_final: 0.8848 (mtp)
REVERT: A  209 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8049 (tp-100)
REVERT: B   16 TYR cc_start: 0.8128 (t80) cc_final: 0.7794 (t80)
REVERT: B  298 TYR cc_start: 0.8972 (t80) cc_final: 0.8485 (t80)
REVERT: B  359 GLU cc_start: 0.7566 (mp0) cc_final: 0.7362 (mp0)
REVERT: B  362 LEU cc_start: 0.8615 (mt) cc_final: 0.7961 (tt)
REVERT: B  383 GLN cc_start: 0.8936 (tt0) cc_final: 0.8718 (mt0)
REVERT: B  388 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8335 (mm-30)
REVERT: B  442 ILE cc_start: 0.8759 (tp) cc_final: 0.8552 (mm)
REVERT: B  447 MET cc_start: 0.7819 (ttt) cc_final: 0.7114 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0716
  time to fit residues: 12.5266
Evaluate side-chains
  112 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 20 optimal weight:    0.7980
   chunk 8 optimal weight:    8.9990
   chunk 42 optimal weight:    0.4980
   chunk 59 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 23 optimal weight:   50.0000
   chunk 66 optimal weight:   40.0000
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.150979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.124585 restraints weight = 12770.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.127699 restraints weight = 7374.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.129687 restraints weight = 5209.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.130299 restraints weight = 4159.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.131516 restraints weight = 3773.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.5190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5074  Z= 0.164
  Angle     :  0.713   9.655   7030  Z= 0.343
  Chirality :  0.045   0.321    964
  Planarity :  0.004   0.037    812
  Dihedral  :  7.417  59.766   1629
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.82 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.34), residues: 670
  helix:  0.87 (0.27), residues: 396
  sheet: -0.22 (0.95), residues: 37
  loop : -2.39 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  31 
 TYR   0.026   0.002   TYR A  88 
 PHE   0.021   0.002   PHE B 435 
 TRP   0.015   0.001   TRP A 146 
 HIS   0.007   0.002   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5072)
  covalent geometry    : angle       0.70638 ( 7024)
  hydrogen bonds       : bond        0.04127 (  289)
  hydrogen bonds       : angle       3.90294 (  852)
  link_BETA1-4         : bond        0.00604 (    1)
  link_BETA1-4         : angle       1.46027 (    3)
  link_NAG-ASN         : bond        0.00883 (    1)
  link_NAG-ASN         : angle       4.66007 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LEU cc_start: 0.9266 (mp) cc_final: 0.9042 (mt)
REVERT: A  132 GLN cc_start: 0.6233 (mm-40) cc_final: 0.6007 (tt0)
REVERT: A  166 THR cc_start: 0.9186 (m) cc_final: 0.8890 (m)
REVERT: A  170 GLN cc_start: 0.8346 (pm20) cc_final: 0.7713 (pm20)
REVERT: A  209 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8100 (tp-100)
REVERT: B   16 TYR cc_start: 0.8077 (t80) cc_final: 0.7784 (t80)
REVERT: B  362 LEU cc_start: 0.8644 (mt) cc_final: 0.8040 (tt)
REVERT: B  388 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8387 (mm-30)
REVERT: B  415 GLN cc_start: 0.7844 (mt0) cc_final: 0.7603 (mt0)
REVERT: B  442 ILE cc_start: 0.8788 (tp) cc_final: 0.8580 (mm)
REVERT: B  630 PHE cc_start: 0.7498 (t80) cc_final: 0.7256 (m-80)
REVERT: B  641 ASN cc_start: 0.5200 (t0) cc_final: 0.4957 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0696
  time to fit residues: 11.7800
Evaluate side-chains
  110 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0060
   chunk 16 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 37 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0270
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.5854

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.151944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.126278 restraints weight = 12790.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.129719 restraints weight = 6901.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.131862 restraints weight = 4675.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.133167 restraints weight = 3638.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.133612 restraints weight = 3109.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.5393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5074  Z= 0.126
  Angle     :  0.687   7.021   7030  Z= 0.329
  Chirality :  0.042   0.297    964
  Planarity :  0.004   0.035    812
  Dihedral  :  7.209  59.823   1629
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  4.33 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.34), residues: 670
  helix:  1.11 (0.27), residues: 396
  sheet: -0.10 (0.95), residues: 37
  loop : -2.32 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 380 
 TYR   0.027   0.001   TYR B 639 
 PHE   0.016   0.001   PHE B 420 
 TRP   0.015   0.001   TRP A 146 
 HIS   0.008   0.002   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5072)
  covalent geometry    : angle       0.68078 ( 7024)
  hydrogen bonds       : bond        0.03940 (  289)
  hydrogen bonds       : angle       3.86671 (  852)
  link_BETA1-4         : bond        0.00088 (    1)
  link_BETA1-4         : angle       1.83662 (    3)
  link_NAG-ASN         : bond        0.00688 (    1)
  link_NAG-ASN         : angle       4.13005 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.7626 (m) cc_final: 0.7325 (p)
REVERT: A   46 LEU cc_start: 0.9294 (mp) cc_final: 0.9065 (mt)
REVERT: A  132 GLN cc_start: 0.6011 (mm-40) cc_final: 0.5752 (tt0)
REVERT: A  133 LEU cc_start: 0.7496 (tp) cc_final: 0.7237 (tp)
REVERT: A  203 MET cc_start: 0.9095 (mtp) cc_final: 0.8834 (mtp)
REVERT: A  209 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8192 (tp-100)
REVERT: B   16 TYR cc_start: 0.8173 (t80) cc_final: 0.7834 (t80)
REVERT: B  298 TYR cc_start: 0.9061 (t80) cc_final: 0.8551 (t80)
REVERT: B  359 GLU cc_start: 0.7480 (mp0) cc_final: 0.7066 (mp0)
REVERT: B  362 LEU cc_start: 0.8615 (mt) cc_final: 0.8010 (tt)
REVERT: B  378 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8705 (mttm)
REVERT: B  383 GLN cc_start: 0.9291 (pt0) cc_final: 0.9085 (pt0)
REVERT: B  388 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8481 (mm-30)
REVERT: B  415 GLN cc_start: 0.7710 (mt0) cc_final: 0.7493 (mt0)
REVERT: B  630 PHE cc_start: 0.7466 (t80) cc_final: 0.7249 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0639
  time to fit residues: 11.3070
Evaluate side-chains
  118 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0770
   chunk 38 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 36 optimal weight:   20.0000
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 53 optimal weight:    9.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.154381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.127094 restraints weight = 12607.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.130623 restraints weight = 7057.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.132800 restraints weight = 4876.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.133959 restraints weight = 3831.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.134765 restraints weight = 3328.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.5622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5074  Z= 0.124
  Angle     :  0.679   8.659   7030  Z= 0.324
  Chirality :  0.043   0.290    964
  Planarity :  0.003   0.035    812
  Dihedral  :  7.086  59.141   1629
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.07 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.34), residues: 670
  helix:  1.18 (0.27), residues: 395
  sheet: -0.14 (0.94), residues: 37
  loop : -2.29 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 380 
 TYR   0.017   0.001   TYR A 180 
 PHE   0.021   0.001   PHE B 435 
 TRP   0.016   0.001   TRP A 146 
 HIS   0.004   0.001   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5072)
  covalent geometry    : angle       0.67350 ( 7024)
  hydrogen bonds       : bond        0.03946 (  289)
  hydrogen bonds       : angle       3.77943 (  852)
  link_BETA1-4         : bond        0.00140 (    1)
  link_BETA1-4         : angle       1.82165 (    3)
  link_NAG-ASN         : bond        0.00688 (    1)
  link_NAG-ASN         : angle       4.00655 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.7587 (m) cc_final: 0.7299 (p)
REVERT: A   46 LEU cc_start: 0.9296 (mp) cc_final: 0.9094 (mt)
REVERT: A  132 GLN cc_start: 0.6010 (mm-40) cc_final: 0.5699 (tt0)
REVERT: A  133 LEU cc_start: 0.7501 (tp) cc_final: 0.7291 (tp)
REVERT: A  209 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8260 (tp-100)
REVERT: B   16 TYR cc_start: 0.8154 (t80) cc_final: 0.7801 (t80)
REVERT: B  298 TYR cc_start: 0.9050 (t80) cc_final: 0.8458 (t80)
REVERT: B  308 MET cc_start: 0.6741 (mtt) cc_final: 0.6476 (mtm)
REVERT: B  359 GLU cc_start: 0.7460 (mp0) cc_final: 0.7050 (mp0)
REVERT: B  362 LEU cc_start: 0.8566 (mt) cc_final: 0.7983 (tt)
REVERT: B  388 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8516 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0640
  time to fit residues: 11.4928
Evaluate side-chains
  114 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 29 optimal weight:   40.0000
   chunk 58 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0050
   chunk 52 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0470
   chunk 10 optimal weight:    0.4980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.4492

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.152668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.127406 restraints weight = 12846.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.130697 restraints weight = 7196.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.132749 restraints weight = 4951.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.133887 restraints weight = 3885.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.134799 restraints weight = 3356.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.5804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5074  Z= 0.121
  Angle     :  0.691   7.802   7030  Z= 0.331
  Chirality :  0.042   0.287    964
  Planarity :  0.003   0.035    812
  Dihedral  :  6.983  58.406   1629
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  4.63 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.35), residues: 670
  helix:  1.34 (0.27), residues: 396
  sheet: -0.14 (0.93), residues: 37
  loop : -2.22 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 380 
 TYR   0.012   0.001   TYR A 180 
 PHE   0.010   0.001   PHE B 301 
 TRP   0.016   0.001   TRP A 146 
 HIS   0.004   0.001   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5072)
  covalent geometry    : angle       0.68566 ( 7024)
  hydrogen bonds       : bond        0.03830 (  289)
  hydrogen bonds       : angle       3.70146 (  852)
  link_BETA1-4         : bond        0.00242 (    1)
  link_BETA1-4         : angle       1.82266 (    3)
  link_NAG-ASN         : bond        0.00649 (    1)
  link_NAG-ASN         : angle       3.86423 (    3)

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.7566 (m) cc_final: 0.7276 (p)
REVERT: A   46 LEU cc_start: 0.9293 (mp) cc_final: 0.9092 (mt)
REVERT: A  132 GLN cc_start: 0.6042 (mm-40) cc_final: 0.5725 (tt0)
REVERT: A  133 LEU cc_start: 0.7539 (tp) cc_final: 0.7244 (tp)
REVERT: A  209 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8297 (tp-100)
REVERT: B   16 TYR cc_start: 0.8091 (t80) cc_final: 0.7739 (t80)
REVERT: B  298 TYR cc_start: 0.9024 (t80) cc_final: 0.8343 (t80)
REVERT: B  308 MET cc_start: 0.6718 (mtt) cc_final: 0.6450 (mtm)
REVERT: B  359 GLU cc_start: 0.7449 (mp0) cc_final: 0.7044 (mp0)
REVERT: B  362 LEU cc_start: 0.8514 (mt) cc_final: 0.7796 (tt)
REVERT: B  378 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8318 (tppt)
REVERT: B  415 GLN cc_start: 0.7231 (mt0) cc_final: 0.6984 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0666
  time to fit residues: 12.0397
Evaluate side-chains
  114 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0270
   chunk 38 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 23 optimal weight:   50.0000
   chunk 53 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0370
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.155947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.128799 restraints weight = 12908.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.132214 restraints weight = 7280.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.134356 restraints weight = 5051.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.135503 restraints weight = 3985.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.136550 restraints weight = 3445.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.5938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   5074  Z= 0.122
  Angle     :  0.673   9.041   7030  Z= 0.327
  Chirality :  0.042   0.287    964
  Planarity :  0.003   0.035    812
  Dihedral  :  6.872  59.172   1629
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  4.93 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.35), residues: 670
  helix:  1.37 (0.27), residues: 400
  sheet: -0.09 (0.93), residues: 37
  loop : -2.12 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 380 
 TYR   0.011   0.001   TYR A  88 
 PHE   0.010   0.001   PHE B 301 
 TRP   0.016   0.001   TRP A 146 
 HIS   0.004   0.001   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5072)
  covalent geometry    : angle       0.66735 ( 7024)
  hydrogen bonds       : bond        0.03807 (  289)
  hydrogen bonds       : angle       3.75201 (  852)
  link_BETA1-4         : bond        0.00424 (    1)
  link_BETA1-4         : angle       1.76914 (    3)
  link_NAG-ASN         : bond        0.00638 (    1)
  link_NAG-ASN         : angle       3.80556 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1028.67 seconds
wall clock time: 18 minutes 18.58 seconds (1098.58 seconds total)