Starting phenix.real_space_refine
on Sun May 11 00:19:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g8w_29857/05_2025/8g8w_29857_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g8w_29857/05_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_29857/05_2025/8g8w_29857.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g8w_29857/05_2025/8g8w_29857.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g8w_29857/05_2025/8g8w_29857_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g8w_29857/05_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-5687/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: 6.49, per 1000 atoms: 1.00
  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: 1.76
  Conformation dependent library (CDL) restraints added in 973.8 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: 0.78
  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: 1.90

  Time building geometry restraints manager: 1.93 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:             8.870
  Set stop_for_unknowns flag:              0.010
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.610
  Find NCS groups from input model:        0.050
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.670
-------------------------------------------------------------------------------
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   6630  Z= 0.192
  Angle     :  0.686  12.609   9086  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 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00106 (    1)
  link_ALPHA1-4        : angle       0.83297 (    3)
  hydrogen bonds       : bond        0.13923 (  363)
  hydrogen bonds       : angle       5.42106 ( 1017)
  SS BOND              : bond        0.00197 (    2)
  SS BOND              : angle       0.29089 (    4)
  covalent geometry    : bond        0.00373 ( 6627)
  covalent geometry    : angle       0.68568 ( 9079)

*********************** 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  : 0.714 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1485
  time to fit residues: 11.8487
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  : 0.658 
-------------------------------------------------------------------------------
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 = 59)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.145996 restraints weight = 10522.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 75)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.142116 restraints weight = 16461.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.141965 restraints weight = 19705.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
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   6630  Z= 0.121
  Angle     :  0.514   7.841   9086  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 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00050 (    1)
  link_ALPHA1-4        : angle       1.25310 (    3)
  hydrogen bonds       : bond        0.04359 (  363)
  hydrogen bonds       : angle       4.52458 ( 1017)
  SS BOND              : bond        0.00238 (    2)
  SS BOND              : angle       0.23808 (    4)
  covalent geometry    : bond        0.00277 ( 6627)
  covalent geometry    : angle       0.51375 ( 9079)

*********************** 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  : 0.709 
Fit side-chains
REVERT: A  292 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8543 (tt)
  outliers start: 8
  outliers final: 5
  residues processed: 60
  average time/residue: 0.1560
  time to fit residues: 13.6723
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  : 0.940 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.155267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 119)---------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.135312 restraints weight = 10710.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.131988 restraints weight = 13162.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.132549 restraints weight = 11731.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.0930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6630  Z= 0.155
  Angle     :  0.535   6.523   9086  Z= 0.269
  Chirality :  0.042   0.169   1043
  Planarity :  0.004   0.054   1152
  Dihedral  : 13.247 176.399   1094
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.24 %
    Favored  : 80.81 %
  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:  2.62 (0.27), residues: 359
  sheet:  0.78 (0.40), residues: 143
  loop : -0.10 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 160 
 PHE   0.010   0.001   PHE A 224 
 TYR   0.009   0.001   TYR A 158 
 ARG   0.004   0.000   ARG B  22 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00092 (    1)
  link_ALPHA1-4        : angle       1.18518 (    3)
  hydrogen bonds       : bond        0.04842 (  363)
  hydrogen bonds       : angle       4.47174 ( 1017)
  SS BOND              : bond        0.00341 (    2)
  SS BOND              : angle       0.33931 (    4)
  covalent geometry    : bond        0.00373 ( 6627)
  covalent geometry    : angle       0.53469 ( 9079)

*********************** 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
  66 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  155 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8594 (m)
REVERT: A  292 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8605 (tt)
REVERT: B  106 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7523 (t80)
  outliers start: 16
  outliers final: 9
  residues processed: 63
  average time/residue: 0.1436
  time to fit residues: 13.1678
Evaluate side-chains
  61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
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 A residue  292 LEU
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0170
   chunk 80 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0020
   chunk 60 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.3826

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.155653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.144815 restraints weight = 10750.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 84)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.140574 restraints weight = 17537.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.140593 restraints weight = 20688.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6630  Z= 0.111
  Angle     :  0.502   6.642   9086  Z= 0.249
  Chirality :  0.041   0.158   1043
  Planarity :  0.004   0.049   1152
  Dihedral  : 12.767 175.404   1094
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.71 %
    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:  1.85 (0.29), residues: 880
  helix:  2.71 (0.27), residues: 360
  sheet:  0.76 (0.40), residues: 143
  loop : -0.03 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 281 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.007   0.001   PHE A 224 
 TYR   0.008   0.001   TYR B 227 
 ARG   0.003   0.000   ARG B  22 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00155 (    1)
  link_ALPHA1-4        : angle       1.30886 (    3)
  hydrogen bonds       : bond        0.04027 (  363)
  hydrogen bonds       : angle       4.26203 ( 1017)
  SS BOND              : bond        0.00232 (    2)
  SS BOND              : angle       0.20811 (    4)
  covalent geometry    : bond        0.00257 ( 6627)
  covalent geometry    : angle       0.50144 ( 9079)

*********************** 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
  64 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7412 (tm-30)
REVERT: A  155 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8573 (m)
REVERT: A  292 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8620 (tt)
REVERT: B  186 ASP cc_start: 0.8210 (p0) cc_final: 0.7997 (p0)
  outliers start: 14
  outliers final: 8
  residues processed: 64
  average time/residue: 0.1559
  time to fit residues: 14.5338
Evaluate side-chains
  58 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
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  292 LEU
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  237 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:    0.8980
   chunk 44 optimal weight:    0.0980
   chunk 65 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   chunk 73 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0050
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5794

-------------------------------------------------------------------------------
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 = 0.3958 r_free = 0.3958 target = 0.154014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.143437 restraints weight = 10606.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.142682 restraints weight = 16239.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142277 restraints weight = 14507.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6630  Z= 0.136
  Angle     :  0.522   6.586   9086  Z= 0.259
  Chirality :  0.041   0.165   1043
  Planarity :  0.004   0.050   1152
  Dihedral  : 12.542 175.572   1094
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  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:  1.82 (0.29), residues: 880
  helix:  2.70 (0.27), residues: 359
  sheet:  0.78 (0.39), residues: 143
  loop : -0.08 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 279 
 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 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00034 (    1)
  link_ALPHA1-4        : angle       1.24232 (    3)
  hydrogen bonds       : bond        0.04332 (  363)
  hydrogen bonds       : angle       4.29509 ( 1017)
  SS BOND              : bond        0.00296 (    2)
  SS BOND              : angle       0.27405 (    4)
  covalent geometry    : bond        0.00326 ( 6627)
  covalent geometry    : angle       0.52148 ( 9079)

*********************** 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  : 0.665 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7415 (tm-30)
REVERT: A  155 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8601 (m)
REVERT: A  168 GLU cc_start: 0.7652 (tp30) cc_final: 0.7413 (tp30)
REVERT: B  186 ASP cc_start: 0.8244 (p0) cc_final: 0.8033 (p0)
  outliers start: 16
  outliers final: 11
  residues processed: 66
  average time/residue: 0.1453
  time to fit residues: 14.0498
Evaluate side-chains
  61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
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 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  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:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 78 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3958 r_free = 0.3958 target = 0.155789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 116)---------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.137287 restraints weight = 10815.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 144)---------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.132572 restraints weight = 14675.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.132354 restraints weight = 14336.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6630  Z= 0.147
  Angle     :  0.534   6.572   9086  Z= 0.266
  Chirality :  0.042   0.166   1043
  Planarity :  0.004   0.049   1152
  Dihedral  : 12.363 175.714   1094
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.71 %
    Favored  : 78.60 %
  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:  1.76 (0.29), residues: 880
  helix:  2.66 (0.27), residues: 358
  sheet:  0.79 (0.40), residues: 143
  loop : -0.13 (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   0.010   0.001   PHE A 224 
 TYR   0.009   0.001   TYR C  97 
 ARG   0.003   0.000   ARG B  22 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00000 (    1)
  link_ALPHA1-4        : angle       1.27135 (    3)
  hydrogen bonds       : bond        0.04524 (  363)
  hydrogen bonds       : angle       4.36377 ( 1017)
  SS BOND              : bond        0.00334 (    2)
  SS BOND              : angle       0.30337 (    4)
  covalent geometry    : bond        0.00355 ( 6627)
  covalent geometry    : angle       0.53369 ( 9079)

*********************** 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
  70 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7455 (tm-30)
REVERT: A  155 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8594 (m)
REVERT: A  168 GLU cc_start: 0.7753 (tp30) cc_final: 0.7531 (tp30)
  outliers start: 20
  outliers final: 12
  residues processed: 68
  average time/residue: 0.1504
  time to fit residues: 14.8424
Evaluate side-chains
  61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
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   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  185 HIS
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   15 VAL
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:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   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:    2.9990
   chunk 85 optimal weight:    7.9990
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.3896 r_free = 0.3896 target = 0.148841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.140800 restraints weight = 10774.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.137056 restraints weight = 15715.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.135737 restraints weight = 23577.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   6630  Z= 0.239
  Angle     :  0.625   6.520   9086  Z= 0.318
  Chirality :  0.044   0.182   1043
  Planarity :  0.005   0.052   1152
  Dihedral  : 12.667 177.709   1094
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 18.82 %
    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:  1.41 (0.28), residues: 880
  helix:  2.41 (0.27), residues: 356
  sheet:  0.67 (0.41), residues: 139
  loop : -0.37 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  39 
 HIS   0.003   0.001   HIS B 160 
 PHE   0.014   0.002   PHE A 224 
 TYR   0.013   0.002   TYR C  97 
 ARG   0.004   0.001   ARG B  22 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00418 (    1)
  link_ALPHA1-4        : angle       1.54317 (    3)
  hydrogen bonds       : bond        0.05706 (  363)
  hydrogen bonds       : angle       4.73059 ( 1017)
  SS BOND              : bond        0.00455 (    2)
  SS BOND              : angle       0.56297 (    4)
  covalent geometry    : bond        0.00587 ( 6627)
  covalent geometry    : angle       0.62459 ( 9079)

*********************** 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
  67 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 0.627 
Fit side-chains
REVERT: A  155 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8781 (m)
REVERT: A  168 GLU cc_start: 0.8079 (tp30) cc_final: 0.7837 (tp30)
REVERT: B  106 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7509 (t80)
  outliers start: 18
  outliers final: 12
  residues processed: 64
  average time/residue: 0.1435
  time to fit residues: 13.3308
Evaluate side-chains
  63 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 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  171 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:    0.4980
   chunk 54 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 50 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0970
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.152670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.141644 restraints weight = 10663.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 84)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.136866 restraints weight = 16922.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.136567 restraints weight = 18927.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6630  Z= 0.126
  Angle     :  0.542   8.428   9086  Z= 0.268
  Chirality :  0.041   0.163   1043
  Planarity :  0.004   0.047   1152
  Dihedral  : 12.135 174.650   1094
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 21.03 %
    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:  1.62 (0.29), residues: 880
  helix:  2.58 (0.28), residues: 357
  sheet:  0.73 (0.40), residues: 139
  loop : -0.23 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   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  98 
 ARG   0.003   0.000   ARG B  22 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00155 (    1)
  link_ALPHA1-4        : angle       1.47661 (    3)
  hydrogen bonds       : bond        0.04427 (  363)
  hydrogen bonds       : angle       4.43054 ( 1017)
  SS BOND              : bond        0.00306 (    2)
  SS BOND              : angle       0.24283 (    4)
  covalent geometry    : bond        0.00293 ( 6627)
  covalent geometry    : angle       0.54194 ( 9079)

*********************** 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
  60 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  155 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8630 (m)
REVERT: A  168 GLU cc_start: 0.7854 (tp30) cc_final: 0.7626 (tp30)
REVERT: A  285 MET cc_start: 0.7855 (tmm) cc_final: 0.7561 (tmm)
REVERT: B  106 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7298 (t80)
  outliers start: 9
  outliers final: 6
  residues processed: 60
  average time/residue: 0.1424
  time to fit residues: 12.8327
Evaluate side-chains
  56 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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  251 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  450 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3949 r_free = 0.3949 target = 0.155061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.140395 restraints weight = 11076.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.137501 restraints weight = 14591.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.134979 restraints weight = 15727.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6630  Z= 0.135
  Angle     :  0.539   7.158   9086  Z= 0.269
  Chirality :  0.041   0.164   1043
  Planarity :  0.004   0.049   1152
  Dihedral  : 11.782 173.957   1094
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 20.48 %
    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:  1.62 (0.29), residues: 880
  helix:  2.57 (0.28), residues: 358
  sheet:  0.69 (0.40), residues: 139
  loop : -0.21 (0.32), residues: 383

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   0.008   0.001   PHE A 224 
 TYR   0.010   0.001   TYR C  82 
 ARG   0.003   0.000   ARG C  22 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00157 (    1)
  link_ALPHA1-4        : angle       1.38864 (    3)
  hydrogen bonds       : bond        0.04381 (  363)
  hydrogen bonds       : angle       4.38208 ( 1017)
  SS BOND              : bond        0.00304 (    2)
  SS BOND              : angle       0.28031 (    4)
  covalent geometry    : bond        0.00323 ( 6627)
  covalent geometry    : angle       0.53892 ( 9079)

*********************** 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
  59 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8652 (m)
REVERT: A  168 GLU cc_start: 0.7958 (tp30) cc_final: 0.7718 (tp30)
REVERT: B  186 ASP cc_start: 0.8306 (p0) cc_final: 0.7994 (p0)
  outliers start: 9
  outliers final: 7
  residues processed: 59
  average time/residue: 0.1388
  time to fit residues: 12.3585
Evaluate side-chains
  57 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0060
   chunk 30 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0870
   chunk 83 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 72 optimal weight:    0.4980
   chunk 80 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 82 optimal weight:    7.9990
   overall best weight:    0.4174

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.156488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.140780 restraints weight = 10935.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.134386 restraints weight = 15768.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.134474 restraints weight = 14415.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6630  Z= 0.121
  Angle     :  0.548  11.210   9086  Z= 0.267
  Chirality :  0.041   0.159   1043
  Planarity :  0.004   0.047   1152
  Dihedral  : 11.361 173.168   1094
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 21.40 %
    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:  1.71 (0.29), residues: 880
  helix:  2.66 (0.28), residues: 358
  sheet:  0.65 (0.39), residues: 143
  loop : -0.15 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  56 
 HIS   0.001   0.001   HIS B 160 
 PHE   0.006   0.001   PHE C  40 
 TYR   0.008   0.001   TYR B 227 
 ARG   0.003   0.000   ARG C  22 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00158 (    1)
  link_ALPHA1-4        : angle       1.26385 (    3)
  hydrogen bonds       : bond        0.04037 (  363)
  hydrogen bonds       : angle       4.30228 ( 1017)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       0.24212 (    4)
  covalent geometry    : bond        0.00288 ( 6627)
  covalent geometry    : angle       0.54770 ( 9079)

********************** 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
  59 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8621 (m)
REVERT: A  168 GLU cc_start: 0.8204 (tp30) cc_final: 0.7977 (tp30)
REVERT: B  186 ASP cc_start: 0.8304 (p0) cc_final: 0.8016 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 59
  average time/residue: 0.1672
  time to fit residues: 14.4093
Evaluate side-chains
  56 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   41 ARG
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  450 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0060
   chunk 49 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0170
   chunk 83 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0470
   chunk 85 optimal weight:    0.0170
   chunk 33 optimal weight:    0.0870
   overall best weight:    0.0348

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.159085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.148435 restraints weight = 10741.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.145747 restraints weight = 17227.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.145422 restraints weight = 17043.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6630  Z= 0.100
  Angle     :  0.520   9.317   9086  Z= 0.254
  Chirality :  0.040   0.148   1043
  Planarity :  0.004   0.048   1152
  Dihedral  : 10.736 171.493   1094
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 22.14 %
    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:  1.93 (0.29), residues: 880
  helix:  2.70 (0.27), residues: 364
  sheet:  0.84 (0.40), residues: 144
  loop :  0.05 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  39 
 HIS   0.001   0.000   HIS A 148 
 PHE   0.004   0.001   PHE C  40 
 TYR   0.007   0.001   TYR B 106 
 ARG   0.007   0.000   ARG C  22 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00419 (    1)
  link_ALPHA1-4        : angle       1.08931 (    3)
  hydrogen bonds       : bond        0.03007 (  363)
  hydrogen bonds       : angle       4.10159 ( 1017)
  SS BOND              : bond        0.00118 (    2)
  SS BOND              : angle       0.23049 (    4)
  covalent geometry    : bond        0.00219 ( 6627)
  covalent geometry    : angle       0.51989 ( 9079)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2494.40 seconds
wall clock time: 44 minutes 19.11 seconds (2659.11 seconds total)