Starting phenix.real_space_refine
on Wed Mar 12 03:00:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g8w_29857/03_2025/8g8w_29857_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g8w_29857/03_2025/8g8w_29857.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g8w_29857/03_2025/8g8w_29857.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g8w_29857/03_2025/8g8w_29857.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g8w_29857/03_2025/8g8w_29857_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g8w_29857/03_2025/8g8w_29857_neut.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      23      5.16       5
     C    4165      2.51       5
     N    1066      2.21       5
     O    1209      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6471
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2146
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 15, 'TRANS': 273}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 2814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 2814
          Classifications: {'peptide': 398}
          Incomplete info: {'truncation_to_alanine': 81}
          Link IDs: {'PTRANS': 24, 'TRANS': 373}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 288
          Unresolved non-hydrogen angles: 348
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 10, 'GLU:plan': 16, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 169
    Chain: "C"
      Number of atoms: 1349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1349
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 97}
          Link IDs: {'PTRANS': 12, 'TRANS': 202}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 335
          Unresolved non-hydrogen angles: 422
          Unresolved non-hydrogen dihedrals: 265
          Unresolved non-hydrogen chiralities: 33
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 179
    Chain: "D"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'GLC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 139
          Unusual residues: {'CDL': 3, 'GTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 193
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 192
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 2, 'CDL:plan-4': 1}
          Unresolved non-hydrogen planarities: 19
  Time building chain proxies: 6.13, per 1000 atoms: 0.95
  Number of scatterers: 6471
  At special positions: 0
  Unit cell: (72.24, 92.02, 203.82, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P       8     15.00
     O    1209      8.00
     N    1066      7.00
     C    4165      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  25 " - pdb=" SG  CYS C  98 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-4
      " GLC D   1 " - " GLC D   2 "
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 944.3 milliseconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1642

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 9 sheets defined
      48.3% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 31
    Processing helix  chain 'A' and resid 31 through 43
      removed outlier: 4.203A  pdb=" N   ASP A  35 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 70
      removed outlier: 3.549A  pdb=" N   GLY A  70 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 88
    Processing helix  chain 'A' and resid 88 through 105
      removed outlier: 4.341A  pdb=" N   ASP A  97 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 130
    Processing helix  chain 'A' and resid 131 through 144
      removed outlier: 4.109A  pdb=" N   GLU A 135 " --> pdb=" O   GLY A 131 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 168
    Processing helix  chain 'A' and resid 176 through 205
      removed outlier: 3.890A  pdb=" N   ASN A 180 " --> pdb=" O   GLY A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 242
      Proline residue:  A 232  - end of helix
    Processing helix  chain 'A' and resid 250 through 262
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 270 through 298
      removed outlier: 4.158A  pdb=" N   LYS A 298 " --> pdb=" O   ARG A 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 35
      removed outlier: 3.931A  pdb=" N   ASN B  34 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR B  35 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 31 through 35'
    Processing helix  chain 'B' and resid 65 through 68
      removed outlier: 4.044A  pdb=" N   GLU B  68 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 65 through 68'
    Processing helix  chain 'B' and resid 90 through 94
      removed outlier: 3.882A  pdb=" N   THR B  94 " --> pdb=" O   PRO B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 153
      removed outlier: 3.594A  pdb=" N   LEU B 141 " --> pdb=" O   GLY B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 172
      Proline residue:  B 169  - end of helix
    Processing helix  chain 'B' and resid 185 through 195
      removed outlier: 4.219A  pdb=" N   GLY B 189 " --> pdb=" O   HIS B 185 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   GLY B 190 " --> pdb=" O   ASP B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 208
    Processing helix  chain 'B' and resid 211 through 217
    Processing helix  chain 'B' and resid 274 through 277
    Processing helix  chain 'B' and resid 278 through 283
      removed outlier: 3.740A  pdb=" N   ILE B 282 " --> pdb=" O   THR B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 340
    Processing helix  chain 'B' and resid 349 through 351
      No H-bonds generated for 'chain 'B' and resid 349 through 351'
    Processing helix  chain 'B' and resid 352 through 359
    Processing helix  chain 'B' and resid 393 through 404
    Processing helix  chain 'B' and resid 407 through 418
      removed outlier: 3.966A  pdb=" N   ASP B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LYS B 418 " --> pdb=" O   VAL B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 433
      removed outlier: 3.650A  pdb=" N   GLU B 431 " --> pdb=" O   SER B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 447
      removed outlier: 3.518A  pdb=" N   LYS B 447 " --> pdb=" O   GLU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 466
      removed outlier: 3.614A  pdb=" N   PHE B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   TRP B 461 " --> pdb=" O   MET B 457 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   TYR B 462 " --> pdb=" O   SER B 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 35
      removed outlier: 3.515A  pdb=" N   TYR C  35 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 93
    Processing helix  chain 'C' and resid 109 through 114
      removed outlier: 3.532A  pdb=" N   TYR C 112 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 156
    Processing helix  chain 'C' and resid 167 through 172
      removed outlier: 3.594A  pdb=" N   PHE C 172 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 397 through 408
      removed outlier: 3.602A  pdb=" N   TYR C 408 " --> pdb=" O   PHE C 404 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14
      removed outlier: 6.723A  pdb=" N   GLY B  13 " --> pdb=" O   THR B 124 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   MET B  37 " --> pdb=" O   ILE B  54 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA B  52 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   ARG B  41 " --> pdb=" O   PHE B  50 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   PHE B  50 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 159
      removed outlier: 6.496A  pdb=" N   LEU B 128 " --> pdb=" O   THR B 157 " (cutoff:3.500A)
      removed outlier: 7.733A  pdb=" N   GLU B 159 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ILE B 130 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE B 180 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ALA B 385 " --> pdb=" O   PRO B 228 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 220
    Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 348
    Processing sheet with id=AA6, first strand: chain 'C' and resid 8 through 10
    Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 14
      removed outlier: 6.813A  pdb=" N   GLY C  13 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   ARG C  41 " --> pdb=" O   PHE C  50 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   PHE C  50 " --> pdb=" O   ARG C  41 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14
      removed outlier: 6.813A  pdb=" N   GLY C  13 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TYR C 120 " --> pdb=" O   ALA C 100 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 163
      removed outlier: 7.536A  pdb=" N   ILE C 134 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LEU C 387 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)

    367 hydrogen bonds defined for protein.
    1017 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: 2.10

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1069
        1.32 -     1.45: 1808
        1.45 -     1.57: 3699
        1.57 -     1.69: 15
        1.69 -     1.82: 36
  Bond restraints: 6627
  Sorted by residual:
  bond pdb=" OA3 CDL A 402 "
       pdb=" PA1 CDL A 402 "
    ideal  model  delta    sigma   weight residual
    1.529  1.503  0.026 1.00e-02 1.00e+04 6.64e+00
  bond pdb=" OB3 CDL A 404 "
       pdb=" PB2 CDL A 404 "
    ideal  model  delta    sigma   weight residual
    1.529  1.503  0.026 1.00e-02 1.00e+04 6.51e+00
  bond pdb=" OB3 CDL A 403 "
       pdb=" PB2 CDL A 403 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.35e+00
  bond pdb=" OA3 CDL A 404 "
       pdb=" PA1 CDL A 404 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.26e+00
  bond pdb=" OA3 CDL A 403 "
       pdb=" PA1 CDL A 403 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.03e+00
  ... (remaining 6622 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 8949
        2.52 -     5.04: 101
        5.04 -     7.57: 18
        7.57 -    10.09: 8
       10.09 -    12.61: 3
  Bond angle restraints: 9079
  Sorted by residual:
  angle pdb=" PA  GTP A 401 "
        pdb=" O3A GTP A 401 "
        pdb=" PB  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     120.50  133.11  -12.61 3.00e+00 1.11e-01 1.77e+01
  angle pdb=" C1' GTP A 401 "
        pdb=" C2' GTP A 401 "
        pdb=" C3' GTP A 401 "
      ideal   model   delta    sigma   weight residual
     111.00   99.26   11.74 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" O1B GTP A 401 "
        pdb=" PB  GTP A 401 "
        pdb=" O2B GTP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50  119.63  -10.13 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" CB  MET B 442 "
        pdb=" CG  MET B 442 "
        pdb=" SD  MET B 442 "
      ideal   model   delta    sigma   weight residual
     112.70  122.34   -9.64 3.00e+00 1.11e-01 1.03e+01
  angle pdb=" PB  GTP A 401 "
        pdb=" O3B GTP A 401 "
        pdb=" PG  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     120.50  130.08   -9.58 3.00e+00 1.11e-01 1.02e+01
  ... (remaining 9074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.44: 3739
       35.44 -    70.89: 115
       70.89 -   106.33: 5
      106.33 -   141.77: 2
      141.77 -   177.22: 2
  Dihedral angle restraints: 3863
    sinusoidal: 1294
      harmonic: 2569
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -78.19 -177.22     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" O3B GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92   83.42 -152.34     1      2.00e+01 2.50e-03 4.53e+01
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     303.79  171.36  132.44     1      2.00e+01 2.50e-03 4.02e+01
  ... (remaining 3860 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 935
       0.070 -    0.140: 100
       0.140 -    0.210: 4
       0.210 -    0.280: 0
       0.280 -    0.350: 4
  Chirality restraints: 1043
  Sorted by residual:
  chirality pdb=" C1  GLC D   1 "
            pdb=" C2  GLC D   1 "
            pdb=" O1  GLC D   1 "
            pdb=" O5  GLC D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.39    0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" C3' GTP A 401 "
            pdb=" C2' GTP A 401 "
            pdb=" C4' GTP A 401 "
            pdb=" O3' GTP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.78    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CA4 CDL A 402 "
            pdb=" CA3 CDL A 402 "
            pdb=" CA6 CDL A 402 "
            pdb=" OA6 CDL A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.57   -2.27   -0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 1040 not shown)

  Planarity restraints: 1152
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  89 "    0.043 5.00e-02 4.00e+02   6.60e-02 6.97e+00
        pdb=" N   PRO C  90 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO C  90 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C  90 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 231 "    0.031 5.00e-02 4.00e+02   4.79e-02 3.67e+00
        pdb=" N   PRO C 232 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO C 232 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 232 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 454 "    0.023 5.00e-02 4.00e+02   3.51e-02 1.97e+00
        pdb=" N   PRO B 455 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 455 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 455 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1149 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1151
        2.77 -     3.30: 5841
        3.30 -     3.83: 10176
        3.83 -     4.37: 10576
        4.37 -     4.90: 19789
  Nonbonded interactions: 47533
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  55 "
            pdb=" OH  TYR C 112 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OD1 ASP B 179 "
            pdb=" OG  SER B 391 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" NE2 GLN A  42 "
            pdb=" OD2 ASP A 234 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" O   ASP C  75 "
            pdb=" N   ASN C  79 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" NZ  LYS A 138 "
            pdb=" O1B GTP A 401 "
     model   vdw
     2.324 3.120
  ... (remaining 47528 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:             7.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     21.280
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6627  Z= 0.266
  Angle     :  0.686  12.609   9079  Z= 0.315
  Chirality :  0.046   0.350   1043
  Planarity :  0.004   0.066   1152
  Dihedral  : 17.422 177.216   2215
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 19.37 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.29), residues: 880
  helix:  2.73 (0.28), residues: 344
  sheet:  0.79 (0.40), residues: 144
  loop : -0.10 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 281 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.008   0.001   PHE A 286 
 TYR   0.011   0.001   TYR C  82 
 ARG   0.002   0.000   ARG A 183 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1501
  time to fit residues: 11.9120
Evaluate side-chains
  50 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0670
   chunk 41 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.4318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.156600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.145101 restraints weight = 10522.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.144331 restraints weight = 17174.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.141453 restraints weight = 16177.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.0634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6627  Z= 0.183
  Angle     :  0.514   7.841   9079  Z= 0.256
  Chirality :  0.041   0.178   1043
  Planarity :  0.004   0.055   1152
  Dihedral  : 14.045 177.565   1094
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.27 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.29), residues: 880
  helix:  2.71 (0.28), residues: 361
  sheet:  0.84 (0.40), residues: 143
  loop : -0.06 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 185 
 PHE   0.007   0.001   PHE B 182 
 TYR   0.008   0.001   TYR B 227 
 ARG   0.004   0.000   ARG B  22 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  292 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8593 (tt)
  outliers start: 8
  outliers final: 5
  residues processed: 60
  average time/residue: 0.1508
  time to fit residues: 13.2338
Evaluate side-chains
  53 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue  237 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
B 207 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.153883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.136319 restraints weight = 10747.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.131150 restraints weight = 15162.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.130948 restraints weight = 14550.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6627  Z= 0.281
  Angle     :  0.557   6.534   9079  Z= 0.282
  Chirality :  0.043   0.172   1043
  Planarity :  0.005   0.056   1152
  Dihedral  : 13.294 176.407   1094
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.42 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.28), residues: 880
  helix:  2.53 (0.27), residues: 359
  sheet:  0.73 (0.40), residues: 143
  loop : -0.16 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 281 
 HIS   0.003   0.001   HIS B 185 
 PHE   0.013   0.001   PHE A 224 
 TYR   0.010   0.001   TYR A 158 
 ARG   0.005   0.001   ARG B  22 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A  155 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8639 (m)
REVERT: B  106 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7500 (t80)
  outliers start: 17
  outliers final: 8
  residues processed: 65
  average time/residue: 0.1589
  time to fit residues: 15.0855
Evaluate side-chains
  60 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  181 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 80 optimal weight:    7.9990
   chunk 36 optimal weight:    0.3980
   chunk 49 optimal weight:    0.6980
   chunk 3 optimal weight:    0.1980
   chunk 60 optimal weight:    0.0170
   chunk 46 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.3418

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

Flipped N/Q/H residues before XYZ refinement:
B 207 GLN
B 403 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.155775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.145066 restraints weight = 10753.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.140687 restraints weight = 17391.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.140000 restraints weight = 17656.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6627  Z= 0.162
  Angle     :  0.503   6.655   9079  Z= 0.248
  Chirality :  0.041   0.156   1043
  Planarity :  0.004   0.049   1152
  Dihedral  : 12.783 175.195   1094
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.63 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.29), residues: 880
  helix:  2.66 (0.27), residues: 359
  sheet:  0.73 (0.39), residues: 143
  loop : -0.02 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 281 
 HIS   0.001   0.000   HIS A 146 
 PHE   0.007   0.001   PHE C  40 
 TYR   0.009   0.001   TYR B 227 
 ARG   0.002   0.000   ARG C  22 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7372 (tm-30)
REVERT: A  155 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8597 (m)
REVERT: C   10 SER cc_start: 0.6380 (m) cc_final: 0.5943 (t)
  outliers start: 10
  outliers final: 5
  residues processed: 60
  average time/residue: 0.1517
  time to fit residues: 13.2424
Evaluate side-chains
  54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   21 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 82 optimal weight:    7.9990
   chunk 73 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0040
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.5192

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.154345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.146049 restraints weight = 10628.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.143302 restraints weight = 15040.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.142693 restraints weight = 19973.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6627  Z= 0.203
  Angle     :  0.512   6.624   9079  Z= 0.256
  Chirality :  0.041   0.164   1043
  Planarity :  0.004   0.050   1152
  Dihedral  : 12.503 175.373   1094
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.34 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.29), residues: 880
  helix:  2.69 (0.27), residues: 359
  sheet:  0.79 (0.39), residues: 143
  loop : -0.07 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  56 
 HIS   0.002   0.001   HIS B 160 
 PHE   0.008   0.001   PHE A 224 
 TYR   0.008   0.001   TYR B 227 
 ARG   0.003   0.000   ARG B  22 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7424 (tm-30)
REVERT: A  155 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8644 (m)
REVERT: A  285 MET cc_start: 0.7930 (tmm) cc_final: 0.7456 (tmm)
REVERT: C   10 SER cc_start: 0.6292 (m) cc_final: 0.5928 (t)
  outliers start: 16
  outliers final: 10
  residues processed: 65
  average time/residue: 0.1413
  time to fit residues: 13.4982
Evaluate side-chains
  61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   21 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 78 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 207 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.152387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.141736 restraints weight = 10648.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.139449 restraints weight = 17580.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.139538 restraints weight = 18955.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6627  Z= 0.252
  Angle     :  0.545   6.607   9079  Z= 0.272
  Chirality :  0.042   0.168   1043
  Planarity :  0.004   0.049   1152
  Dihedral  : 12.462 175.983   1094
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 17.71 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.29), residues: 880
  helix:  2.67 (0.27), residues: 357
  sheet:  0.74 (0.39), residues: 143
  loop : -0.15 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  56 
 HIS   0.002   0.001   HIS B 160 
 PHE   0.010   0.001   PHE A 224 
 TYR   0.010   0.001   TYR C  97 
 ARG   0.004   0.000   ARG B  22 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8652 (m)
REVERT: A  168 GLU cc_start: 0.7791 (tp30) cc_final: 0.7551 (tp30)
REVERT: B  186 ASP cc_start: 0.8288 (p0) cc_final: 0.8015 (p0)
REVERT: C   10 SER cc_start: 0.6347 (m) cc_final: 0.5997 (t)
  outliers start: 18
  outliers final: 12
  residues processed: 69
  average time/residue: 0.1505
  time to fit residues: 15.2494
Evaluate side-chains
  63 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  185 HIS
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   21 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 77 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.151835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.140988 restraints weight = 10610.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.136122 restraints weight = 17588.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.135548 restraints weight = 20070.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6627  Z= 0.262
  Angle     :  0.554   6.599   9079  Z= 0.278
  Chirality :  0.042   0.168   1043
  Planarity :  0.004   0.051   1152
  Dihedral  : 12.341 175.847   1094
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.82 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.29), residues: 880
  helix:  2.61 (0.27), residues: 357
  sheet:  0.73 (0.40), residues: 143
  loop : -0.21 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  56 
 HIS   0.002   0.001   HIS B 160 
 PHE   0.010   0.001   PHE A 224 
 TYR   0.010   0.001   TYR C  97 
 ARG   0.004   0.000   ARG B  22 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8663 (m)
REVERT: A  168 GLU cc_start: 0.8029 (tp30) cc_final: 0.7774 (tp30)
REVERT: A  285 MET cc_start: 0.7954 (tmm) cc_final: 0.7509 (tmm)
REVERT: C   10 SER cc_start: 0.6475 (m) cc_final: 0.5940 (t)
  outliers start: 16
  outliers final: 12
  residues processed: 66
  average time/residue: 0.1414
  time to fit residues: 13.6603
Evaluate side-chains
  62 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  185 HIS
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   15 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 26 optimal weight:    0.0670
   chunk 54 optimal weight:    7.9990
   chunk 6 optimal weight:    0.6980
   chunk 51 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.5118

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.155929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 131)---------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.138160 restraints weight = 10876.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.137953 restraints weight = 16095.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 81)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.135189 restraints weight = 15050.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6627  Z= 0.202
  Angle     :  0.538   6.623   9079  Z= 0.269
  Chirality :  0.041   0.161   1043
  Planarity :  0.004   0.049   1152
  Dihedral  : 11.960 174.268   1094
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.56 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.29), residues: 880
  helix:  2.68 (0.28), residues: 358
  sheet:  0.72 (0.39), residues: 143
  loop : -0.20 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  56 
 HIS   0.002   0.001   HIS B 160 
 PHE   0.014   0.001   PHE C  70 
 TYR   0.011   0.001   TYR C  82 
 ARG   0.009   0.000   ARG C  22 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8646 (m)
REVERT: A  168 GLU cc_start: 0.8086 (tp30) cc_final: 0.7856 (tp30)
REVERT: A  285 MET cc_start: 0.7875 (tmm) cc_final: 0.7348 (tmm)
REVERT: B  186 ASP cc_start: 0.8433 (p0) cc_final: 0.8107 (p0)
REVERT: C   10 SER cc_start: 0.6405 (m) cc_final: 0.6052 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 63
  average time/residue: 0.1485
  time to fit residues: 13.6421
Evaluate side-chains
  60 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   15 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.2980
   chunk 63 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 403 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.153548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.142664 restraints weight = 10881.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 78)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.138531 restraints weight = 17436.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.137459 restraints weight = 21423.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6627  Z= 0.201
  Angle     :  0.536   7.156   9079  Z= 0.268
  Chirality :  0.041   0.162   1043
  Planarity :  0.004   0.049   1152
  Dihedral  : 11.516 173.162   1094
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.48 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.29), residues: 880
  helix:  2.71 (0.28), residues: 358
  sheet:  0.72 (0.39), residues: 143
  loop : -0.18 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  56 
 HIS   0.002   0.001   HIS B 160 
 PHE   0.007   0.001   PHE A 224 
 TYR   0.009   0.001   TYR B 227 
 ARG   0.003   0.000   ARG B  22 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7371 (tm-30)
REVERT: A  155 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8630 (m)
REVERT: A  168 GLU cc_start: 0.8089 (tp30) cc_final: 0.7831 (tp30)
REVERT: C   10 SER cc_start: 0.6264 (m) cc_final: 0.5942 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 60
  average time/residue: 0.1576
  time to fit residues: 13.6371
Evaluate side-chains
  60 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   15 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 51 optimal weight:    0.3980
   chunk 83 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 82 optimal weight:    7.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.151927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.142480 restraints weight = 10744.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.138261 restraints weight = 15214.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.136054 restraints weight = 21958.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6627  Z= 0.246
  Angle     :  0.559   7.643   9079  Z= 0.281
  Chirality :  0.042   0.167   1043
  Planarity :  0.005   0.049   1152
  Dihedral  : 11.409 174.963   1094
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.48 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.29), residues: 880
  helix:  2.67 (0.28), residues: 357
  sheet:  0.68 (0.39), residues: 143
  loop : -0.25 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  56 
 HIS   0.002   0.001   HIS B 160 
 PHE   0.009   0.001   PHE A 224 
 TYR   0.010   0.001   TYR B 227 
 ARG   0.009   0.001   ARG C  22 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A  155 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8704 (m)
REVERT: A  168 GLU cc_start: 0.8045 (tp30) cc_final: 0.7803 (tp30)
REVERT: A  285 MET cc_start: 0.7908 (tmm) cc_final: 0.7483 (tmm)
REVERT: B  106 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7381 (t80)
REVERT: C   10 SER cc_start: 0.6226 (m) cc_final: 0.5930 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 63
  average time/residue: 0.1536
  time to fit residues: 13.9548
Evaluate side-chains
  60 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   15 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    0.0970
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 49 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0980
   chunk 83 optimal weight:    0.0570
   chunk 45 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.2496

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

Flipped N/Q/H residues before XYZ refinement:
B 207 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.158058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 130)---------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.140216 restraints weight = 10982.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 79)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.135551 restraints weight = 16052.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.134249 restraints weight = 15059.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6627  Z= 0.163
  Angle     :  0.526   7.718   9079  Z= 0.262
  Chirality :  0.040   0.153   1043
  Planarity :  0.004   0.047   1152
  Dihedral  : 11.074 173.204   1094
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 22.14 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.29), residues: 880
  helix:  2.74 (0.28), residues: 359
  sheet:  0.70 (0.39), residues: 143
  loop : -0.09 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  39 
 HIS   0.001   0.000   HIS A 146 
 PHE   0.006   0.001   PHE C  40 
 TYR   0.007   0.001   TYR B 227 
 ARG   0.011   0.000   ARG C  22 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2496.78 seconds
wall clock time: 43 minutes 45.84 seconds (2625.84 seconds total)