Starting phenix.real_space_refine
on Sat May 10 02:32:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vhg_43237/05_2025/8vhg_43237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vhg_43237/05_2025/8vhg_43237.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vhg_43237/05_2025/8vhg_43237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vhg_43237/05_2025/8vhg_43237.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vhg_43237/05_2025/8vhg_43237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vhg_43237/05_2025/8vhg_43237.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
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      36      5.49       5
     S      28      5.16       5
     C    2880      2.51       5
     N     844      2.21       5
     O     931      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4719
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2271
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 9, 'TRANS': 276}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 1710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1710
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 4, 'TRANS': 221}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 125
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 90
    Chain: "C"
      Number of atoms: 366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 366
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "D"
      Number of atoms: 372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 372
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
  Time building chain proxies: 3.58, per 1000 atoms: 0.76
  Number of scatterers: 4719
  At special positions: 0
  Unit cell: (113.22, 106.08, 86.7, 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      28     16.00
     P      36     15.00
     O     931      8.00
     N     844      7.00
     C    2880      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 461.4 milliseconds
  

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  986

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 5 sheets defined
      35.2% alpha, 12.7% beta
      17 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 1.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 40
      removed outlier: 4.048A  pdb=" N   LYS A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLU A  40 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 69
      removed outlier: 3.756A  pdb=" N   ILE A  56 " --> pdb=" O   ASP A  52 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   MET A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ARG A  58 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 118
      removed outlier: 3.835A  pdb=" N   SER A 116 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE A 118 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 127
      removed outlier: 4.283A  pdb=" N   THR A 127 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 134
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 3.877A  pdb=" N   THR A 148 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 265
      removed outlier: 4.270A  pdb=" N   LEU A 264 " --> pdb=" O   ARG A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 299
      removed outlier: 4.447A  pdb=" N   GLU A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   LYS A 291 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 99
      removed outlier: 4.014A  pdb=" N   LEU B  95 " --> pdb=" O   PHE B  91 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   ALA B  96 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   SER B  97 " --> pdb=" O   ASP B  93 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   LEU B  98 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 124
      removed outlier: 3.904A  pdb=" N   LYS B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   THR B 124 " --> pdb=" O   GLN B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 155
      removed outlier: 5.101A  pdb=" N   ARG B 153 " --> pdb=" O   HIS B 149 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ALA B 155 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 196
      removed outlier: 3.532A  pdb=" N   LEU B 196 " --> pdb=" O   PHE B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 207
    Processing helix  chain 'B' and resid 356 through 361
    Processing helix  chain 'B' and resid 372 through 377
      removed outlier: 4.490A  pdb=" N   TYR B 376 " --> pdb=" O   SER B 372 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE B 377 " --> pdb=" O   CYS B 373 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 372 through 377'
    Processing helix  chain 'B' and resid 381 through 394
      removed outlier: 3.681A  pdb=" N   LEU B 385 " --> pdb=" O   ASP B 381 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   GLN B 394 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111
      removed outlier: 7.108A  pdb=" N   VAL A 101 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   LEU A 111 " --> pdb=" O   ILE A  99 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE A  99 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE A  98 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLN A 198 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   CYS A 195 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 168 " --> pdb=" O   CYS A 195 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 257
      removed outlier: 4.071A  pdb=" N   SER A 246 " --> pdb=" O   CYS A 339 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   CYS A 339 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ILE A 337 " --> pdb=" O   HIS A 248 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   MET A 338 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL A 340 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLN A 322 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   VAL A 302 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 310
      removed outlier: 3.909A  pdb=" N   TYR A 307 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL A 317 " --> pdb=" O   MET A 309 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 172
      removed outlier: 4.510A  pdb=" N   PHE B 171 " --> pdb=" O   VAL B 161 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE B 160 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA B 316 " --> pdb=" O   PHE B 160 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 424
      removed outlier: 3.598A  pdb=" N   PHE B 421 " --> pdb=" O   VAL B 435 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL B 435 " --> pdb=" O   PHE B 421 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   TYR B 433 " --> pdb=" O   PHE B 423 " (cutoff:3.500A)

    127 hydrogen bonds defined for protein.
    357 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      46 hydrogen bonds
      92 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 1.43

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1393
        1.34 -     1.46: 1333
        1.46 -     1.58: 2039
        1.58 -     1.71: 69
        1.71 -     1.83: 44
  Bond restraints: 4878
  Sorted by residual:
  bond pdb=" O5'  DG C  12 "
       pdb=" C5'  DG C  12 "
    ideal  model  delta    sigma   weight residual
    1.423  1.361  0.062 3.00e-02 1.11e+03 4.24e+00
  bond pdb=" P    DG C  12 "
       pdb=" O5'  DG C  12 "
    ideal  model  delta    sigma   weight residual
    1.600  1.564  0.036 2.00e-02 2.50e+03 3.18e+00
  bond pdb=" C   PRO A 334 "
       pdb=" O   PRO A 334 "
    ideal  model  delta    sigma   weight residual
    1.235  1.247 -0.012 7.90e-03 1.60e+04 2.18e+00
  bond pdb=" C5'  DG C  12 "
       pdb=" C4'  DG C  12 "
    ideal  model  delta    sigma   weight residual
    1.518  1.489  0.029 2.00e-02 2.50e+03 2.05e+00
  bond pdb=" CB  ARG A  15 "
       pdb=" CG  ARG A  15 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 2.00e+00
  ... (remaining 4873 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 6534
        1.80 -     3.61: 157
        3.61 -     5.41: 26
        5.41 -     7.21: 8
        7.21 -     9.02: 2
  Bond angle restraints: 6727
  Sorted by residual:
  angle pdb=" N   GLY A  97 "
        pdb=" CA  GLY A  97 "
        pdb=" C   GLY A  97 "
      ideal   model   delta    sigma   weight residual
     111.21  114.85   -3.64 1.04e+00 9.25e-01 1.23e+01
  angle pdb=" O5'  DG C  12 "
        pdb=" C5'  DG C  12 "
        pdb=" C4'  DG C  12 "
      ideal   model   delta    sigma   weight residual
     110.80  105.93    4.87 1.50e+00 4.44e-01 1.05e+01
  angle pdb=" OP2  DG C  12 "
        pdb=" P    DG C  12 "
        pdb=" O5'  DG C  12 "
      ideal   model   delta    sigma   weight residual
     108.00   98.98    9.02 3.00e+00 1.11e-01 9.03e+00
  angle pdb=" N   GLY A 266 "
        pdb=" CA  GLY A 266 "
        pdb=" C   GLY A 266 "
      ideal   model   delta    sigma   weight residual
     113.18  119.29   -6.11 2.37e+00 1.78e-01 6.66e+00
  angle pdb=" N   LEU B 196 "
        pdb=" CA  LEU B 196 "
        pdb=" CB  LEU B 196 "
      ideal   model   delta    sigma   weight residual
     111.05  107.47    3.58 1.50e+00 4.44e-01 5.69e+00
  ... (remaining 6722 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 2278
       17.32 -    34.64: 325
       34.64 -    51.96: 149
       51.96 -    69.28: 52
       69.28 -    86.59: 2
  Dihedral angle restraints: 2806
    sinusoidal: 1307
      harmonic: 1499
  Sorted by residual:
  dihedral pdb=" CA  THR B 401 "
           pdb=" C   THR B 401 "
           pdb=" N   ASN B 402 "
           pdb=" CA  ASN B 402 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.18   22.82     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASN B 402 "
           pdb=" C   ASN B 402 "
           pdb=" N   CYS B 403 "
           pdb=" CA  CYS B 403 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.20  -19.80     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  SER B 418 "
           pdb=" C   SER B 418 "
           pdb=" N   ARG B 419 "
           pdb=" CA  ARG B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.97   19.03     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 2803 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 489
       0.035 -    0.069: 197
       0.069 -    0.104: 60
       0.104 -    0.139: 21
       0.139 -    0.174: 3
  Chirality restraints: 770
  Sorted by residual:
  chirality pdb=" CG  LEU A 222 "
            pdb=" CB  LEU A 222 "
            pdb=" CD1 LEU A 222 "
            pdb=" CD2 LEU A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.53e-01
  chirality pdb=" CA  VAL A 199 "
            pdb=" N   VAL A 199 "
            pdb=" C   VAL A 199 "
            pdb=" CB  VAL A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.43e-01
  chirality pdb=" CB  VAL A 199 "
            pdb=" CA  VAL A 199 "
            pdb=" CG1 VAL A 199 "
            pdb=" CG2 VAL A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.27e-01
  ... (remaining 767 not shown)

  Planarity restraints: 720
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 425 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO B 426 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 426 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 426 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  24 "   -0.168 9.50e-02 1.11e+02   7.52e-02 3.52e+00
        pdb=" NE  ARG A  24 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  24 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  24 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  24 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 268 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO A 269 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 269 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 269 "    0.026 5.00e-02 4.00e+02
  ... (remaining 717 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1274
        2.82 -     3.34: 4296
        3.34 -     3.86: 7422
        3.86 -     4.38: 8100
        4.38 -     4.90: 12698
  Nonbonded interactions: 33790
  Sorted by model distance:
  nonbonded pdb=" O5'  DG C  12 "
            pdb=" O4'  DG C  12 "
     model   vdw
     2.303 2.432
  nonbonded pdb=" O5'  DC D   4 "
            pdb=" O4'  DC D   4 "
     model   vdw
     2.502 2.432
  nonbonded pdb=" O5'  DG C   3 "
            pdb=" O4'  DG C   3 "
     model   vdw
     2.511 2.432
  nonbonded pdb=" O5'  DT C  13 "
            pdb=" O4'  DT C  13 "
     model   vdw
     2.538 2.432
  nonbonded pdb=" O5'  DG C  16 "
            pdb=" O4'  DG C  16 "
     model   vdw
     2.546 2.432
  ... (remaining 33785 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:             1.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.960
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6560
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   0.062   4878  Z= 0.204
  Angle     :  0.727   9.017   6727  Z= 0.398
  Chirality :  0.043   0.174    770
  Planarity :  0.007   0.075    720
  Dihedral  : 20.382  86.594   1820
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  :  4.12 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.37), residues: 482
  helix: -0.58 (0.43), residues: 140
  sheet: -2.41 (0.47), residues: 99
  loop : -2.45 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 318 
 HIS   0.006   0.001   HIS A 268 
 PHE   0.014   0.002   PHE B 171 
 TYR   0.016   0.002   TYR B 287 
 ARG   0.009   0.001   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17228 (  173)
  hydrogen bonds       : angle       7.31331 (  449)
  covalent geometry    : bond        0.00423 ( 4878)
  covalent geometry    : angle       0.72679 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 VAL cc_start: 0.6727 (m) cc_final: 0.6490 (t)
REVERT: A  191 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6220 (mttt)
REVERT: A  256 TYR cc_start: 0.6646 (t80) cc_final: 0.5887 (t80)
REVERT: A  273 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6249 (mm)
REVERT: A  287 GLU cc_start: 0.8028 (pp20) cc_final: 0.7628 (pp20)
REVERT: B   91 PHE cc_start: 0.6909 (m-80) cc_final: 0.6509 (m-10)
REVERT: B  184 GLN cc_start: 0.7629 (mm-40) cc_final: 0.6451 (pt0)
REVERT: B  338 MET cc_start: 0.7024 (tpp) cc_final: 0.6601 (mmm)
  outliers start: 11
  outliers final: 6
  residues processed: 125
  average time/residue: 0.2240
  time to fit residues: 33.4581
Evaluate side-chains
  118 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue  343 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    0.2980
   chunk 39 optimal weight:    0.0270
   chunk 21 optimal weight:    0.0870
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0970
   chunk 40 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.1614

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.114658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.105276 restraints weight = 16343.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.107180 restraints weight = 9615.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.108441 restraints weight = 6212.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4878  Z= 0.138
  Angle     :  0.599   6.778   6727  Z= 0.326
  Chirality :  0.039   0.131    770
  Planarity :  0.004   0.039    720
  Dihedral  : 22.006  83.073    939
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 14.29 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.38), residues: 482
  helix:  0.05 (0.43), residues: 135
  sheet: -2.25 (0.47), residues: 104
  loop : -2.01 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 190 
 HIS   0.009   0.001   HIS A 136 
 PHE   0.015   0.001   PHE A 244 
 TYR   0.005   0.001   TYR A 307 
 ARG   0.004   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05215 (  173)
  hydrogen bonds       : angle       5.34957 (  449)
  covalent geometry    : bond        0.00275 ( 4878)
  covalent geometry    : angle       0.59900 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7237 (pp)
REVERT: A   47 VAL cc_start: 0.6715 (m) cc_final: 0.6484 (t)
REVERT: A  191 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6261 (mttt)
REVERT: A  225 MET cc_start: 0.5342 (mmm) cc_final: 0.5110 (mmm)
REVERT: A  256 TYR cc_start: 0.6380 (t80) cc_final: 0.5743 (t80)
REVERT: A  273 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5930 (mm)
REVERT: A  287 GLU cc_start: 0.7963 (pp20) cc_final: 0.7598 (pp20)
REVERT: B   87 LYS cc_start: 0.7997 (mmmm) cc_final: 0.7085 (pttm)
REVERT: B  338 MET cc_start: 0.6897 (tpp) cc_final: 0.6463 (mmm)
  outliers start: 18
  outliers final: 7
  residues processed: 120
  average time/residue: 0.2105
  time to fit residues: 30.2451
Evaluate side-chains
  116 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 19 optimal weight:    0.0060
   chunk 20 optimal weight:    0.3980
   chunk 29 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   overall best weight:    0.2592

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.114535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.105124 restraints weight = 16434.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.107048 restraints weight = 9562.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.108316 restraints weight = 6135.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6524
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4878  Z= 0.124
  Angle     :  0.585  10.229   6727  Z= 0.312
  Chirality :  0.039   0.128    770
  Planarity :  0.004   0.036    720
  Dihedral  : 21.697  78.557    933
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 17.19 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.38), residues: 482
  helix:  0.22 (0.43), residues: 142
  sheet: -2.07 (0.47), residues: 104
  loop : -2.00 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 420 
 HIS   0.007   0.001   HIS A 136 
 PHE   0.021   0.001   PHE A 110 
 TYR   0.008   0.001   TYR A 281 
 ARG   0.004   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04369 (  173)
  hydrogen bonds       : angle       4.87926 (  449)
  covalent geometry    : bond        0.00263 ( 4878)
  covalent geometry    : angle       0.58487 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6902 (pp)
REVERT: A  191 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6416 (mttt)
REVERT: A  287 GLU cc_start: 0.7956 (pp20) cc_final: 0.7638 (pp20)
REVERT: B   83 ARG cc_start: 0.7248 (mtm110) cc_final: 0.6964 (mtm110)
REVERT: B   87 LYS cc_start: 0.7863 (mmmm) cc_final: 0.7199 (pttm)
REVERT: B  184 GLN cc_start: 0.7496 (mm-40) cc_final: 0.6315 (pt0)
REVERT: B  338 MET cc_start: 0.6883 (tpp) cc_final: 0.6440 (mmm)
  outliers start: 18
  outliers final: 12
  residues processed: 116
  average time/residue: 0.2208
  time to fit residues: 30.7034
Evaluate side-chains
  117 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 16 optimal weight:    0.0970
   chunk 37 optimal weight:    0.0030
   chunk 51 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0040
   chunk 36 optimal weight:    0.0980
   chunk 21 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0050
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.0414

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.116516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.107205 restraints weight = 16578.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.109103 restraints weight = 9648.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.110372 restraints weight = 6210.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6457
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4878  Z= 0.112
  Angle     :  0.532   5.896   6727  Z= 0.289
  Chirality :  0.038   0.137    770
  Planarity :  0.003   0.035    720
  Dihedral  : 21.505  74.379    933
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.31 %
    Favored  : 75.30 %
  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: -1.68 (0.39), residues: 482
  helix:  0.55 (0.43), residues: 142
  sheet: -1.71 (0.47), residues: 105
  loop : -1.87 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 190 
 HIS   0.003   0.001   HIS A 136 
 PHE   0.012   0.001   PHE B 421 
 TYR   0.008   0.001   TYR A 267 
 ARG   0.002   0.000   ARG B 343 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  173)
  hydrogen bonds       : angle       4.47377 (  449)
  covalent geometry    : bond        0.00228 ( 4878)
  covalent geometry    : angle       0.53170 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6117 (pp)
REVERT: A  191 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6470 (mttt)
REVERT: A  192 VAL cc_start: 0.8332 (p) cc_final: 0.7978 (m)
REVERT: A  271 GLU cc_start: 0.6242 (pt0) cc_final: 0.5868 (pm20)
REVERT: A  273 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5496 (mp)
REVERT: A  287 GLU cc_start: 0.7949 (pp20) cc_final: 0.7680 (pp20)
REVERT: B   83 ARG cc_start: 0.7320 (mtm110) cc_final: 0.7119 (mtm110)
REVERT: B   87 LYS cc_start: 0.7816 (mmmm) cc_final: 0.7003 (pttm)
REVERT: B  184 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6201 (pt0)
REVERT: B  314 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7267 (tp)
REVERT: B  338 MET cc_start: 0.6798 (tpp) cc_final: 0.6337 (mmm)
  outliers start: 14
  outliers final: 8
  residues processed: 122
  average time/residue: 0.2260
  time to fit residues: 32.8465
Evaluate side-chains
  118 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 16 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
B 391 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.112019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.102473 restraints weight = 16645.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.104399 restraints weight = 9578.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.105714 restraints weight = 6136.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4878  Z= 0.188
  Angle     :  0.634   5.306   6727  Z= 0.348
  Chirality :  0.040   0.124    770
  Planarity :  0.004   0.035    720
  Dihedral  : 21.481  69.911    929
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 23.00 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.39), residues: 482
  helix:  0.30 (0.44), residues: 147
  sheet: -1.49 (0.52), residues: 94
  loop : -2.11 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 318 
 HIS   0.007   0.002   HIS A  50 
 PHE   0.013   0.002   PHE A 110 
 TYR   0.012   0.001   TYR A 307 
 ARG   0.004   0.000   ARG B  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05228 (  173)
  hydrogen bonds       : angle       4.72224 (  449)
  covalent geometry    : bond        0.00417 ( 4878)
  covalent geometry    : angle       0.63375 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6763 (pp)
REVERT: A  191 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.6388 (mttt)
REVERT: A  192 VAL cc_start: 0.8351 (p) cc_final: 0.8070 (m)
REVERT: A  271 GLU cc_start: 0.6418 (pt0) cc_final: 0.6197 (tp30)
REVERT: A  287 GLU cc_start: 0.7978 (pp20) cc_final: 0.7730 (pp20)
REVERT: B   87 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7125 (ptpp)
REVERT: B  184 GLN cc_start: 0.7790 (mm-40) cc_final: 0.6723 (pt0)
REVERT: B  338 MET cc_start: 0.6979 (tpp) cc_final: 0.6525 (mmm)
  outliers start: 19
  outliers final: 15
  residues processed: 119
  average time/residue: 0.2188
  time to fit residues: 31.2797
Evaluate side-chains
  127 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  195 TYR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 10 optimal weight:    0.2980
   chunk 39 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0770
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.112408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.102914 restraints weight = 16489.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.104820 restraints weight = 9579.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.106107 restraints weight = 6144.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6586
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4878  Z= 0.156
  Angle     :  0.603   5.663   6727  Z= 0.330
  Chirality :  0.040   0.123    770
  Planarity :  0.004   0.038    720
  Dihedral  : 21.536  72.273    929
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.73 %
    Favored  : 71.43 %
  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 (0.39), residues: 482
  helix:  0.37 (0.45), residues: 147
  sheet: -1.47 (0.52), residues: 95
  loop : -2.14 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 420 
 HIS   0.006   0.001   HIS A 136 
 PHE   0.011   0.002   PHE A 244 
 TYR   0.009   0.001   TYR A 307 
 ARG   0.002   0.000   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04835 (  173)
  hydrogen bonds       : angle       4.72295 (  449)
  covalent geometry    : bond        0.00342 ( 4878)
  covalent geometry    : angle       0.60309 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6235 (pp)
REVERT: A  191 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6388 (mttt)
REVERT: A  192 VAL cc_start: 0.8352 (p) cc_final: 0.8066 (m)
REVERT: A  271 GLU cc_start: 0.6389 (pt0) cc_final: 0.6159 (tp30)
REVERT: A  287 GLU cc_start: 0.7996 (pp20) cc_final: 0.7615 (pp20)
REVERT: B   87 LYS cc_start: 0.7800 (mmmm) cc_final: 0.7079 (ptpp)
REVERT: B  184 GLN cc_start: 0.7764 (mm-40) cc_final: 0.6688 (pt0)
REVERT: B  338 MET cc_start: 0.6970 (tpp) cc_final: 0.6516 (mmm)
  outliers start: 20
  outliers final: 17
  residues processed: 120
  average time/residue: 0.2216
  time to fit residues: 31.9898
Evaluate side-chains
  126 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  138 CYS
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0010
   chunk 36 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0070
   overall best weight:    0.3604

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.113177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.103969 restraints weight = 16563.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.105796 restraints weight = 9616.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.107011 restraints weight = 6182.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4878  Z= 0.130
  Angle     :  0.584   6.369   6727  Z= 0.318
  Chirality :  0.039   0.121    770
  Planarity :  0.004   0.041    720
  Dihedral  : 21.528  70.255    929
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.97 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.77 (0.39), residues: 482
  helix:  0.22 (0.44), residues: 153
  sheet: -1.34 (0.52), residues: 95
  loop : -2.08 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 318 
 HIS   0.005   0.001   HIS A 136 
 PHE   0.010   0.001   PHE A 244 
 TYR   0.011   0.001   TYR B 340 
 ARG   0.006   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  173)
  hydrogen bonds       : angle       4.46404 (  449)
  covalent geometry    : bond        0.00283 ( 4878)
  covalent geometry    : angle       0.58398 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.5999 (pp)
REVERT: A  191 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6504 (mttt)
REVERT: A  192 VAL cc_start: 0.8323 (p) cc_final: 0.8032 (m)
REVERT: A  287 GLU cc_start: 0.7989 (pp20) cc_final: 0.7623 (pp20)
REVERT: B   87 LYS cc_start: 0.7771 (mmmm) cc_final: 0.7168 (pttm)
REVERT: B  184 GLN cc_start: 0.7690 (mm-40) cc_final: 0.6616 (pt0)
REVERT: B  314 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7256 (tp)
REVERT: B  338 MET cc_start: 0.6915 (tpp) cc_final: 0.6490 (mmm)
  outliers start: 20
  outliers final: 15
  residues processed: 117
  average time/residue: 0.2154
  time to fit residues: 30.3966
Evaluate side-chains
  124 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  138 CYS
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.111701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.102291 restraints weight = 16492.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.104190 restraints weight = 9557.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.105458 restraints weight = 6104.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6605
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4878  Z= 0.171
  Angle     :  0.653   7.957   6727  Z= 0.352
  Chirality :  0.041   0.162    770
  Planarity :  0.004   0.043    720
  Dihedral  : 21.523  71.819    929
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 24.70 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.79 (0.38), residues: 482
  helix:  0.36 (0.45), residues: 147
  sheet: -1.34 (0.51), residues: 95
  loop : -2.15 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 420 
 HIS   0.006   0.001   HIS A 136 
 PHE   0.011   0.002   PHE B 177 
 TYR   0.010   0.001   TYR A 307 
 ARG   0.003   0.000   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05021 (  173)
  hydrogen bonds       : angle       4.59025 (  449)
  covalent geometry    : bond        0.00379 ( 4878)
  covalent geometry    : angle       0.65305 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6160 (pp)
REVERT: A  287 GLU cc_start: 0.8017 (pp20) cc_final: 0.7680 (pp20)
REVERT: B   87 LYS cc_start: 0.7898 (mmmm) cc_final: 0.7198 (pttm)
REVERT: B  184 GLN cc_start: 0.7833 (mm-40) cc_final: 0.6814 (pt0)
REVERT: B  338 MET cc_start: 0.6998 (tpp) cc_final: 0.6582 (mmm)
  outliers start: 20
  outliers final: 16
  residues processed: 113
  average time/residue: 0.2184
  time to fit residues: 30.0854
Evaluate side-chains
  119 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  138 CYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0980
   chunk 35 optimal weight:    0.0870
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.112639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.103659 restraints weight = 16809.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.105508 restraints weight = 9818.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.106724 restraints weight = 6319.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6570
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4878  Z= 0.139
  Angle     :  0.612   8.200   6727  Z= 0.327
  Chirality :  0.040   0.160    770
  Planarity :  0.004   0.042    720
  Dihedral  : 21.534  69.757    925
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 24.94 %
    Favored  : 70.70 %
  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: -1.77 (0.38), residues: 482
  helix:  0.19 (0.44), residues: 153
  sheet: -1.20 (0.52), residues: 93
  loop : -2.12 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 420 
 HIS   0.004   0.001   HIS A 136 
 PHE   0.011   0.001   PHE A 244 
 TYR   0.008   0.001   TYR B 340 
 ARG   0.002   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04385 (  173)
  hydrogen bonds       : angle       4.45782 (  449)
  covalent geometry    : bond        0.00304 ( 4878)
  covalent geometry    : angle       0.61243 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6131 (pp)
REVERT: A  287 GLU cc_start: 0.8012 (pp20) cc_final: 0.7706 (pp20)
REVERT: B   87 LYS cc_start: 0.7807 (mmmm) cc_final: 0.7144 (pttm)
REVERT: B  184 GLN cc_start: 0.7802 (mm-40) cc_final: 0.6794 (pt0)
REVERT: B  314 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7303 (tp)
REVERT: B  338 MET cc_start: 0.6978 (tpp) cc_final: 0.6549 (mmm)
  outliers start: 18
  outliers final: 15
  residues processed: 113
  average time/residue: 0.2109
  time to fit residues: 28.7172
Evaluate side-chains
  119 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  138 CYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0870
   chunk 31 optimal weight:    0.0170
   chunk 45 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0030
   chunk 24 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0070
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.1224

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.114837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.105651 restraints weight = 16419.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.107523 restraints weight = 9632.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.108747 restraints weight = 6234.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6505
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4878  Z= 0.123
  Angle     :  0.619   8.617   6727  Z= 0.325
  Chirality :  0.039   0.148    770
  Planarity :  0.004   0.043    720
  Dihedral  : 21.460  65.026    925
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 26.15 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.57 (0.38), residues: 482
  helix:  0.31 (0.44), residues: 153
  sheet: -1.08 (0.51), residues: 95
  loop : -1.96 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 190 
 HIS   0.004   0.001   HIS B 384 
 PHE   0.010   0.001   PHE A 244 
 TYR   0.010   0.001   TYR B 340 
 ARG   0.004   0.000   ARG B 250 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03485 (  173)
  hydrogen bonds       : angle       4.22453 (  449)
  covalent geometry    : bond        0.00259 ( 4878)
  covalent geometry    : angle       0.61908 ( 6727)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.5697 (pp)
REVERT: A  287 GLU cc_start: 0.8044 (pp20) cc_final: 0.7670 (pp20)
REVERT: A  296 LEU cc_start: 0.5748 (tp) cc_final: 0.5465 (tt)
REVERT: B   87 LYS cc_start: 0.7753 (mmmm) cc_final: 0.7158 (pttm)
REVERT: B  184 GLN cc_start: 0.7627 (mm-40) cc_final: 0.6507 (pt0)
REVERT: B  314 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7225 (tp)
  outliers start: 14
  outliers final: 11
  residues processed: 111
  average time/residue: 0.1988
  time to fit residues: 27.0856
Evaluate side-chains
  109 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 26 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0770
   chunk 37 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.113043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.103603 restraints weight = 16485.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.105516 restraints weight = 9566.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.106783 restraints weight = 6144.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4878  Z= 0.149
  Angle     :  0.618   7.828   6727  Z= 0.333
  Chirality :  0.040   0.139    770
  Planarity :  0.004   0.040    720
  Dihedral  : 21.404  65.092    925
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 26.39 %
    Favored  : 69.49 %
  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: -1.63 (0.38), residues: 482
  helix:  0.27 (0.45), residues: 153
  sheet: -1.10 (0.51), residues: 95
  loop : -2.02 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 420 
 HIS   0.005   0.001   HIS B 384 
 PHE   0.013   0.001   PHE A 244 
 TYR   0.010   0.001   TYR B 195 
 ARG   0.005   0.000   ARG A 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04313 (  173)
  hydrogen bonds       : angle       4.34069 (  449)
  covalent geometry    : bond        0.00329 ( 4878)
  covalent geometry    : angle       0.61831 ( 6727)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2012.89 seconds
wall clock time: 35 minutes 43.59 seconds (2143.59 seconds total)