Starting phenix.real_space_refine
on Wed Feb 12 01:35:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dsw_30848/02_2025/7dsw_30848.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dsw_30848/02_2025/7dsw_30848.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dsw_30848/02_2025/7dsw_30848.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dsw_30848/02_2025/7dsw_30848.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dsw_30848/02_2025/7dsw_30848.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dsw_30848/02_2025/7dsw_30848.cif"
  }
  resolution = 3.3
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    4584      2.51       5
     N    1012      2.21       5
     O    1098      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6720
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3301
          Classifications: {'peptide': 420}
          Link IDs: {'PTRANS': 15, 'TRANS': 404}
    Chain: "B"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 59
          Unusual residues: {'LBN': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 253
          Unresolved non-hydrogen angles: 307
          Unresolved non-hydrogen dihedrals: 235
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 3, 'LBN:plan-1': 6}
          Unresolved non-hydrogen planarities: 56
    Chain: "A"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 59
          Unusual residues: {'LBN': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 253
          Unresolved non-hydrogen angles: 307
          Unresolved non-hydrogen dihedrals: 235
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 3, 'LBN:plan-1': 6}
          Unresolved non-hydrogen planarities: 56
  Restraints were copied for chains:
    B
  Residues with excluded nonbonded symmetry interactions: 12
    residue:
      pdb=" C10 LBN B 601 " occ=0.00
      ... (7 atoms not shown)
      pdb=" C7  LBN B 601 " occ=0.00
    residue:
      pdb=" C35 LBN B 602 " occ=0.00
      ... (7 atoms not shown)
      pdb=" C5  LBN B 602 " occ=0.00
    residue:
      pdb=" C11 LBN B 603 " occ=0.00
      ... (9 atoms not shown)
      pdb=" C8  LBN B 603 " occ=0.00
    residue:
      pdb=" C11 LBN B 604 " occ=0.00
      ... (9 atoms not shown)
      pdb=" C8  LBN B 604 " occ=0.00
    residue:
      pdb=" C11 LBN B 605 " occ=0.00
      ... (4 atoms not shown)
      pdb=" C23 LBN B 605 " occ=0.00
    residue:
      pdb=" C11 LBN B 606 " occ=0.00
      ... (11 atoms not shown)
      pdb=" C8  LBN B 606 " occ=0.00
    residue:
      pdb=" C11 LBN A 801 " occ=0.00
      ... (11 atoms not shown)
      pdb=" C8  LBN A 801 " occ=0.00
    residue:
      pdb=" C10 LBN A 802 " occ=0.00
      ... (7 atoms not shown)
      pdb=" C7  LBN A 802 " occ=0.00
    residue:
      pdb=" C35 LBN A 803 " occ=0.00
      ... (7 atoms not shown)
      pdb=" C5  LBN A 803 " occ=0.00
    residue:
      pdb=" C11 LBN A 804 " occ=0.00
      ... (9 atoms not shown)
      pdb=" C8  LBN A 804 " occ=0.00
    residue:
      pdb=" C11 LBN A 805 " occ=0.00
      ... (9 atoms not shown)
      pdb=" C8  LBN A 805 " occ=0.00
    residue:
      pdb=" C11 LBN A 806 " occ=0.00
      ... (4 atoms not shown)
      pdb=" C23 LBN A 806 " occ=0.00
  Time building chain proxies: 5.87, per 1000 atoms: 0.87
  Number of scatterers: 6720
  At special positions: 0
  Unit cell: (113.36, 67.6, 68.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      26     16.00
     O    1098      8.00
     N    1012      7.00
     C    4584      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: 1.83
  Conformation dependent library (CDL) restraints added in 889.1 milliseconds
  

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      77.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'B' and resid 100 through 121
      removed outlier: 3.752A  pdb=" N   VAL B 121 " --> pdb=" O   ILE B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 150
      removed outlier: 3.747A  pdb=" N   LEU B 134 " --> pdb=" O   PRO B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 165
    Processing helix  chain 'B' and resid 165 through 176
      removed outlier: 3.921A  pdb=" N   ILE B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 184
      No H-bonds generated for 'chain 'B' and resid 182 through 184'
    Processing helix  chain 'B' and resid 185 through 215
    Processing helix  chain 'B' and resid 224 through 235
      removed outlier: 3.728A  pdb=" N   LEU B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   PHE B 230 " --> pdb=" O   ASP B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 246
      removed outlier: 3.868A  pdb=" N   ALA B 244 " --> pdb=" O   ALA B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 281
      removed outlier: 3.685A  pdb=" N   HIS B 256 " --> pdb=" O   ASN B 252 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B 257 " --> pdb=" O   GLU B 253 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL B 271 " --> pdb=" O   ASP B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 321
    Processing helix  chain 'B' and resid 329 through 348
      removed outlier: 3.833A  pdb=" N   PHE B 348 " --> pdb=" O   SER B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 367
      Proline residue:  B 365  - end of helix
    Processing helix  chain 'B' and resid 372 through 404
    Processing helix  chain 'B' and resid 410 through 437
    Processing helix  chain 'B' and resid 445 through 454
    Processing helix  chain 'B' and resid 461 through 468
    Processing helix  chain 'B' and resid 476 through 494
    Processing helix  chain 'B' and resid 499 through 505
      removed outlier: 3.754A  pdb=" N   ASP B 504 " --> pdb=" O   ARG B 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 121
      removed outlier: 3.751A  pdb=" N   VAL A 121 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 150
      removed outlier: 3.747A  pdb=" N   LEU A 134 " --> pdb=" O   PRO A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 165
    Processing helix  chain 'A' and resid 165 through 176
      removed outlier: 3.921A  pdb=" N   ILE A 169 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE A 176 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 184
      No H-bonds generated for 'chain 'A' and resid 182 through 184'
    Processing helix  chain 'A' and resid 185 through 215
    Processing helix  chain 'A' and resid 224 through 235
      removed outlier: 3.728A  pdb=" N   LEU A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   PHE A 230 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 246
      removed outlier: 3.868A  pdb=" N   ALA A 244 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 281
      removed outlier: 3.685A  pdb=" N   HIS A 256 " --> pdb=" O   ASN A 252 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE A 257 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 321
    Processing helix  chain 'A' and resid 329 through 348
      removed outlier: 3.834A  pdb=" N   PHE A 348 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 367
      Proline residue:  A 365  - end of helix
    Processing helix  chain 'A' and resid 372 through 404
    Processing helix  chain 'A' and resid 410 through 437
    Processing helix  chain 'A' and resid 445 through 454
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 476 through 494
    Processing helix  chain 'A' and resid 499 through 505
      removed outlier: 3.753A  pdb=" N   ASP A 504 " --> pdb=" O   ARG A 500 " (cutoff:3.500A)

    478 hydrogen bonds defined for protein.
    1404 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 2.02 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: 1951
        1.34 -     1.46: 1348
        1.46 -     1.57: 3551
        1.57 -     1.69: 0
        1.69 -     1.80: 42
  Bond restraints: 6892
  Sorted by residual:
  bond pdb=" C41 LBN B 606 "
       pdb=" C42 LBN B 606 "
    ideal  model  delta    sigma   weight residual
    1.497  1.568 -0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" C5  LBN B 603 "
       pdb=" C8  LBN B 603 "
    ideal  model  delta    sigma   weight residual
    1.497  1.567 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" C41 LBN A 801 "
       pdb=" C42 LBN A 801 "
    ideal  model  delta    sigma   weight residual
    1.497  1.567 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C5  LBN A 804 "
       pdb=" C8  LBN A 804 "
    ideal  model  delta    sigma   weight residual
    1.497  1.567 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C41 LBN A 803 "
       pdb=" C42 LBN A 803 "
    ideal  model  delta    sigma   weight residual
    1.497  1.567 -0.070 2.00e-02 2.50e+03 1.22e+01
  ... (remaining 6887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 8885
        1.76 -     3.52: 342
        3.52 -     5.28: 93
        5.28 -     7.03: 24
        7.03 -     8.79: 6
  Bond angle restraints: 9350
  Sorted by residual:
  angle pdb=" N   ILE B 125 "
        pdb=" CA  ILE B 125 "
        pdb=" C   ILE B 125 "
      ideal   model   delta    sigma   weight residual
     113.71  108.01    5.70 9.50e-01 1.11e+00 3.60e+01
  angle pdb=" N   ILE A 125 "
        pdb=" CA  ILE A 125 "
        pdb=" C   ILE A 125 "
      ideal   model   delta    sigma   weight residual
     113.71  108.01    5.70 9.50e-01 1.11e+00 3.60e+01
  angle pdb=" CA  TRP B 386 "
        pdb=" CB  TRP B 386 "
        pdb=" CG  TRP B 386 "
      ideal   model   delta    sigma   weight residual
     113.60  119.18   -5.58 1.90e+00 2.77e-01 8.62e+00
  angle pdb=" CA  TRP A 386 "
        pdb=" CB  TRP A 386 "
        pdb=" CG  TRP A 386 "
      ideal   model   delta    sigma   weight residual
     113.60  119.17   -5.57 1.90e+00 2.77e-01 8.61e+00
  angle pdb=" CB  MET A 208 "
        pdb=" CG  MET A 208 "
        pdb=" SD  MET A 208 "
      ideal   model   delta    sigma   weight residual
     112.70  121.49   -8.79 3.00e+00 1.11e-01 8.59e+00
  ... (remaining 9345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.86: 3398
       14.86 -    29.72: 388
       29.72 -    44.59: 106
       44.59 -    59.45: 18
       59.45 -    74.31: 10
  Dihedral angle restraints: 3920
    sinusoidal: 1512
      harmonic: 2408
  Sorted by residual:
  dihedral pdb=" CA  TYR A 366 "
           pdb=" C   TYR A 366 "
           pdb=" N   VAL A 367 "
           pdb=" CA  VAL A 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.29   19.71     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  TYR B 366 "
           pdb=" C   TYR B 366 "
           pdb=" N   VAL B 367 "
           pdb=" CA  VAL B 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.29   19.71     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  ASN B 252 "
           pdb=" C   ASN B 252 "
           pdb=" N   GLU B 253 "
           pdb=" CA  GLU B 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.32   15.68     0      5.00e+00 4.00e-02 9.83e+00
  ... (remaining 3917 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 650
       0.033 -    0.067: 306
       0.067 -    0.100: 120
       0.100 -    0.134: 36
       0.134 -    0.167: 8
  Chirality restraints: 1120
  Sorted by residual:
  chirality pdb=" CA  PRO B 167 "
            pdb=" N   PRO B 167 "
            pdb=" C   PRO B 167 "
            pdb=" CB  PRO B 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.01e-01
  chirality pdb=" CA  PRO A 167 "
            pdb=" N   PRO A 167 "
            pdb=" C   PRO A 167 "
            pdb=" CB  PRO A 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 6.83e-01
  chirality pdb=" CB  THR A 124 "
            pdb=" CA  THR A 124 "
            pdb=" OG1 THR A 124 "
            pdb=" CG2 THR A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.53e-01
  ... (remaining 1117 not shown)

  Planarity restraints: 1122
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 445 "   -0.032 5.00e-02 4.00e+02   4.85e-02 3.77e+00
        pdb=" N   PRO B 446 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 446 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 446 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 445 "    0.032 5.00e-02 4.00e+02   4.83e-02 3.74e+00
        pdb=" N   PRO A 446 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 446 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 446 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 161 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   PHE B 161 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE B 161 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE B 162 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1119 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1194
        2.76 -     3.29: 6696
        3.29 -     3.83: 11443
        3.83 -     4.36: 12816
        4.36 -     4.90: 23226
  Nonbonded interactions: 55375
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 440 "
            pdb=" NZ  LYS A 443 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" O   ARG B 440 "
            pdb=" NZ  LYS B 443 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O   VAL A 494 "
            pdb=" OG1 THR A 498 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   VAL B 494 "
            pdb=" OG1 THR B 498 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG1 THR B 445 "
            pdb=" OD1 ASP B 448 "
     model   vdw
     2.292 3.040
  ... (remaining 55370 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 87 through 506 or resid 802 or (resid 803 and (name C40 or \ 
 name C41 or name C42 or name C5 )) or resid 804 or (resid 805 through 806 and ( \ 
name C11 or name C14 or name C17 or name C20 or name C22 or name C23))))
  selection = (chain 'B' and (resid 87 through 506 or resid 602 or (resid 603 and (name C40 or \ 
 name C41 or name C42 or name C5 )) or resid 604 through 605 or (resid 606 and ( \ 
name C11 or name C14 or name C17 or name C20 or name C22 or name C23))))
}

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=0.00 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     20.050
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
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      :  0.008   0.071   6892  Z= 0.496
  Angle     :  0.896   8.793   9350  Z= 0.457
  Chirality :  0.047   0.167   1120
  Planarity :  0.005   0.049   1122
  Dihedral  : 14.346  74.310   2376
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  0.00 %
    Favored  : 98.89 %
  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: -0.48 (0.29), residues: 836
  helix:  0.58 (0.20), residues: 642
  sheet:  None (None), residues: 0
  loop : -3.35 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 386 
 HIS   0.007   0.001   HIS A 250 
 PHE   0.020   0.002   PHE A 176 
 TYR   0.014   0.002   TYR A 274 
 ARG   0.009   0.001   ARG B 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 154
  time to evaluate  : 0.655 
Fit side-chains
REVERT: B  335 PHE cc_start: 0.8217 (m-80) cc_final: 0.7778 (m-80)
REVERT: B  416 SER cc_start: 0.8889 (t) cc_final: 0.8542 (t)
REVERT: B  457 LEU cc_start: 0.8142 (pp) cc_final: 0.7920 (pp)
REVERT: B  476 MET cc_start: 0.7118 (mmt) cc_final: 0.6904 (pmm)
REVERT: A  416 SER cc_start: 0.8891 (t) cc_final: 0.8536 (t)
  outliers start: 8
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1570
  time to fit residues: 34.3327
Evaluate side-chains
  128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 49 optimal weight:    0.2980
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  98 HIS
B 220 ASN
B 250 HIS
A  98 HIS
A 220 ASN
A 250 HIS
A 495 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.123143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.105957 restraints weight = 8495.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.82
r_work: 0.3094 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6892  Z= 0.232
  Angle     :  0.598   6.340   9350  Z= 0.314
  Chirality :  0.042   0.207   1120
  Planarity :  0.004   0.045   1122
  Dihedral  :  8.103  65.747    958
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.00 %
    Favored  : 89.34 %
  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:  0.24 (0.30), residues: 836
  helix:  1.19 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -3.47 (0.36), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 386 
 HIS   0.005   0.001   HIS A 325 
 PHE   0.020   0.001   PHE B 295 
 TYR   0.017   0.002   TYR B  96 
 ARG   0.006   0.000   ARG A 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.739 
Fit side-chains
REVERT: B  234 ILE cc_start: 0.8706 (tt) cc_final: 0.8477 (tt)
REVERT: B  247 GLU cc_start: 0.7728 (pm20) cc_final: 0.7474 (pm20)
REVERT: B  364 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7666 (tpt-90)
REVERT: B  368 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7332 (mt-10)
REVERT: B  384 LYS cc_start: 0.8708 (tppt) cc_final: 0.8377 (mmtt)
REVERT: B  416 SER cc_start: 0.8986 (t) cc_final: 0.8639 (t)
REVERT: B  448 ASP cc_start: 0.8223 (p0) cc_final: 0.7992 (p0)
REVERT: B  457 LEU cc_start: 0.8405 (pp) cc_final: 0.8189 (pp)
REVERT: B  476 MET cc_start: 0.7650 (mmt) cc_final: 0.7042 (pmm)
REVERT: A  234 ILE cc_start: 0.8661 (tt) cc_final: 0.8392 (tt)
REVERT: A  247 GLU cc_start: 0.7787 (pm20) cc_final: 0.7528 (pm20)
REVERT: A  416 SER cc_start: 0.8973 (t) cc_final: 0.8634 (t)
REVERT: A  448 ASP cc_start: 0.8165 (p0) cc_final: 0.7942 (p0)
REVERT: A  476 MET cc_start: 0.7692 (mmt) cc_final: 0.7142 (pmm)
  outliers start: 12
  outliers final: 9
  residues processed: 150
  average time/residue: 0.1581
  time to fit residues: 33.0965
Evaluate side-chains
  146 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  481 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 75 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 28 optimal weight:    0.3980
   chunk 52 optimal weight:    0.7980
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN
B 250 HIS
A 220 ASN
A 250 HIS
** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.124920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.108382 restraints weight = 8582.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.77
r_work: 0.3108 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6892  Z= 0.237
  Angle     :  0.572   6.100   9350  Z= 0.302
  Chirality :  0.042   0.223   1120
  Planarity :  0.004   0.045   1122
  Dihedral  :  7.324  66.367    958
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.30 %
    Favored  : 84.63 %
  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:  0.71 (0.30), residues: 836
  helix:  1.56 (0.21), residues: 626
  sheet:  None (None), residues: 0
  loop : -3.03 (0.37), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 386 
 HIS   0.003   0.001   HIS A 376 
 PHE   0.019   0.001   PHE A 295 
 TYR   0.014   0.001   TYR B  96 
 ARG   0.004   0.000   ARG A 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.693 
Fit side-chains
REVERT: B  234 ILE cc_start: 0.8761 (tt) cc_final: 0.8530 (tt)
REVERT: B  299 PHE cc_start: 0.7912 (m-10) cc_final: 0.7676 (m-80)
REVERT: B  335 PHE cc_start: 0.8345 (m-80) cc_final: 0.8075 (m-80)
REVERT: B  364 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7706 (tpt-90)
REVERT: B  368 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7370 (mt-10)
REVERT: B  448 ASP cc_start: 0.8197 (p0) cc_final: 0.7964 (p0)
REVERT: B  476 MET cc_start: 0.7614 (mmt) cc_final: 0.7037 (pmm)
REVERT: A  234 ILE cc_start: 0.8691 (tt) cc_final: 0.8412 (tt)
REVERT: A  247 GLU cc_start: 0.7830 (pm20) cc_final: 0.7556 (pm20)
REVERT: A  335 PHE cc_start: 0.8385 (m-80) cc_final: 0.8004 (m-80)
REVERT: A  448 ASP cc_start: 0.8254 (p0) cc_final: 0.8009 (p0)
REVERT: A  476 MET cc_start: 0.7681 (mmt) cc_final: 0.7119 (pmm)
  outliers start: 15
  outliers final: 11
  residues processed: 143
  average time/residue: 0.1491
  time to fit residues: 30.4585
Evaluate side-chains
  143 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  385 MET
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  481 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
A 250 HIS
** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.129143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.113064 restraints weight = 8576.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.73
r_work: 0.3100 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6892  Z= 0.237
  Angle     :  0.567   6.055   9350  Z= 0.298
  Chirality :  0.042   0.232   1120
  Planarity :  0.005   0.046   1122
  Dihedral  :  6.903  68.153    958
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.13 %
    Favored  : 83.24 %
  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:  0.90 (0.30), residues: 836
  helix:  1.75 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop : -3.04 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 386 
 HIS   0.004   0.001   HIS A 376 
 PHE   0.019   0.001   PHE A 295 
 TYR   0.013   0.001   TYR A 274 
 ARG   0.004   0.000   ARG A 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.673 
Fit side-chains
REVERT: B  234 ILE cc_start: 0.8769 (tt) cc_final: 0.8532 (tt)
REVERT: B  278 GLU cc_start: 0.8563 (tt0) cc_final: 0.8115 (mt-10)
REVERT: B  299 PHE cc_start: 0.7865 (m-10) cc_final: 0.7628 (m-80)
REVERT: B  335 PHE cc_start: 0.8403 (m-80) cc_final: 0.8097 (m-80)
REVERT: B  435 PHE cc_start: 0.8400 (t80) cc_final: 0.8163 (t80)
REVERT: B  448 ASP cc_start: 0.8172 (p0) cc_final: 0.7936 (p0)
REVERT: B  476 MET cc_start: 0.7629 (mmt) cc_final: 0.7046 (pmm)
REVERT: A  234 ILE cc_start: 0.8784 (tt) cc_final: 0.8530 (tt)
REVERT: A  247 GLU cc_start: 0.7831 (pm20) cc_final: 0.7626 (pm20)
REVERT: A  278 GLU cc_start: 0.8477 (tt0) cc_final: 0.8045 (mt-10)
REVERT: A  335 PHE cc_start: 0.8423 (m-80) cc_final: 0.8061 (m-80)
REVERT: A  448 ASP cc_start: 0.8238 (p0) cc_final: 0.7999 (p0)
REVERT: A  476 MET cc_start: 0.7650 (mmt) cc_final: 0.7052 (pmm)
  outliers start: 19
  outliers final: 17
  residues processed: 142
  average time/residue: 0.1473
  time to fit residues: 29.9096
Evaluate side-chains
  148 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 GLN
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain B residue  385 MET
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  481 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
A 250 HIS
** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.128489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.112333 restraints weight = 8475.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 1.69
r_work: 0.3090 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6892  Z= 0.250
  Angle     :  0.569   6.085   9350  Z= 0.300
  Chirality :  0.042   0.242   1120
  Planarity :  0.005   0.049   1122
  Dihedral  :  6.866  67.262    958
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 15.24 %
    Favored  : 80.75 %
  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:  0.93 (0.30), residues: 836
  helix:  1.74 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.97 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 386 
 HIS   0.003   0.001   HIS B 250 
 PHE   0.019   0.001   PHE A 295 
 TYR   0.012   0.001   TYR B 283 
 ARG   0.005   0.000   ARG B 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.748 
Fit side-chains
REVERT: B  192 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7987 (t80)
REVERT: B  234 ILE cc_start: 0.8793 (tt) cc_final: 0.8575 (tt)
REVERT: B  278 GLU cc_start: 0.8545 (tt0) cc_final: 0.8102 (mt-10)
REVERT: B  299 PHE cc_start: 0.7848 (m-10) cc_final: 0.7640 (m-80)
REVERT: B  335 PHE cc_start: 0.8387 (m-80) cc_final: 0.8055 (m-80)
REVERT: B  435 PHE cc_start: 0.8473 (t80) cc_final: 0.8126 (t80)
REVERT: B  448 ASP cc_start: 0.8196 (p0) cc_final: 0.7955 (p0)
REVERT: B  476 MET cc_start: 0.7640 (mmt) cc_final: 0.7063 (pmm)
REVERT: A  192 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7943 (t80)
REVERT: A  234 ILE cc_start: 0.8786 (tt) cc_final: 0.8561 (tt)
REVERT: A  247 GLU cc_start: 0.7871 (pm20) cc_final: 0.7621 (pm20)
REVERT: A  278 GLU cc_start: 0.8522 (tt0) cc_final: 0.8044 (mt-10)
REVERT: A  335 PHE cc_start: 0.8384 (m-80) cc_final: 0.8094 (m-80)
REVERT: A  448 ASP cc_start: 0.8227 (p0) cc_final: 0.7974 (p0)
REVERT: A  476 MET cc_start: 0.7666 (mmt) cc_final: 0.7066 (pmm)
  outliers start: 29
  outliers final: 21
  residues processed: 151
  average time/residue: 0.1446
  time to fit residues: 31.2897
Evaluate side-chains
  154 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 GLN
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain B residue  385 MET
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  481 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
B 266 ASN
A 250 HIS
A 266 ASN
** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.122153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.105352 restraints weight = 8693.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.80
r_work: 0.3086 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6892  Z= 0.236
  Angle     :  0.560   5.985   9350  Z= 0.296
  Chirality :  0.042   0.247   1120
  Planarity :  0.005   0.049   1122
  Dihedral  :  6.829  66.747    958
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 15.93 %
    Favored  : 80.19 %
  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:  0.98 (0.30), residues: 836
  helix:  1.77 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.93 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 386 
 HIS   0.003   0.001   HIS B 250 
 PHE   0.020   0.001   PHE A 295 
 TYR   0.011   0.001   TYR B 274 
 ARG   0.003   0.000   ARG A 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.717 
Fit side-chains
REVERT: B  192 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7989 (t80)
REVERT: B  234 ILE cc_start: 0.8807 (tt) cc_final: 0.8572 (tt)
REVERT: B  278 GLU cc_start: 0.8549 (tt0) cc_final: 0.8114 (mt-10)
REVERT: B  299 PHE cc_start: 0.7807 (m-10) cc_final: 0.7562 (m-80)
REVERT: B  335 PHE cc_start: 0.8366 (m-80) cc_final: 0.8016 (m-80)
REVERT: B  448 ASP cc_start: 0.8205 (p0) cc_final: 0.7961 (p0)
REVERT: B  476 MET cc_start: 0.7615 (mmt) cc_final: 0.7023 (pmm)
REVERT: A  192 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7970 (t80)
REVERT: A  234 ILE cc_start: 0.8799 (tt) cc_final: 0.8550 (tt)
REVERT: A  247 GLU cc_start: 0.7906 (pm20) cc_final: 0.7505 (pm20)
REVERT: A  278 GLU cc_start: 0.8530 (tt0) cc_final: 0.8045 (mt-10)
REVERT: A  335 PHE cc_start: 0.8443 (m-80) cc_final: 0.8068 (m-80)
REVERT: A  356 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8749 (tt)
REVERT: A  435 PHE cc_start: 0.8379 (t80) cc_final: 0.8153 (t80)
REVERT: A  448 ASP cc_start: 0.8238 (p0) cc_final: 0.7975 (p0)
REVERT: A  476 MET cc_start: 0.7679 (mmt) cc_final: 0.7039 (pmm)
  outliers start: 28
  outliers final: 22
  residues processed: 148
  average time/residue: 0.1410
  time to fit residues: 29.9967
Evaluate side-chains
  156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 GLN
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain B residue  385 MET
Chi-restraints excluded: chain B residue  391 GLU
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  481 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:    0.4980
   chunk 55 optimal weight:    0.0970
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
A 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.125117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.108861 restraints weight = 8524.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.74
r_work: 0.3123 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6892  Z= 0.187
  Angle     :  0.540   6.679   9350  Z= 0.285
  Chirality :  0.041   0.260   1120
  Planarity :  0.005   0.049   1122
  Dihedral  :  6.504  64.103    958
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.45 %
    Favored  : 79.36 %
  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:  1.20 (0.31), residues: 836
  helix:  1.93 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.82 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 386 
 HIS   0.002   0.001   HIS B 250 
 PHE   0.017   0.001   PHE A 295 
 TYR   0.010   0.001   TYR A 274 
 ARG   0.006   0.000   ARG B 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.775 
Fit side-chains
REVERT: B  192 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8066 (t80)
REVERT: B  234 ILE cc_start: 0.8776 (tt) cc_final: 0.8499 (tt)
REVERT: B  278 GLU cc_start: 0.8516 (tt0) cc_final: 0.8022 (mt-10)
REVERT: B  299 PHE cc_start: 0.7737 (m-10) cc_final: 0.7523 (m-80)
REVERT: B  335 PHE cc_start: 0.8311 (m-80) cc_final: 0.8009 (m-80)
REVERT: B  356 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8727 (tt)
REVERT: B  448 ASP cc_start: 0.8195 (p0) cc_final: 0.7957 (p0)
REVERT: B  476 MET cc_start: 0.7614 (mmt) cc_final: 0.7029 (pmm)
REVERT: A  192 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.8080 (t80)
REVERT: A  234 ILE cc_start: 0.8778 (tt) cc_final: 0.8490 (tt)
REVERT: A  247 GLU cc_start: 0.7924 (pm20) cc_final: 0.7557 (pm20)
REVERT: A  278 GLU cc_start: 0.8413 (tt0) cc_final: 0.7933 (mt-10)
REVERT: A  335 PHE cc_start: 0.8385 (m-80) cc_final: 0.8115 (m-80)
REVERT: A  382 PHE cc_start: 0.7807 (t80) cc_final: 0.7462 (t80)
REVERT: A  448 ASP cc_start: 0.8225 (p0) cc_final: 0.7974 (p0)
REVERT: A  476 MET cc_start: 0.7646 (mmt) cc_final: 0.7034 (pmm)
  outliers start: 23
  outliers final: 10
  residues processed: 145
  average time/residue: 0.1483
  time to fit residues: 31.3237
Evaluate side-chains
  144 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain B residue  391 GLU
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain A residue  391 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0970
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0870
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.127568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.111378 restraints weight = 8523.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.74
r_work: 0.3128 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6892  Z= 0.194
  Angle     :  0.555   7.534   9350  Z= 0.295
  Chirality :  0.042   0.266   1120
  Planarity :  0.005   0.048   1122
  Dihedral  :  6.454  64.404    958
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.59 %
    Favored  : 79.50 %
  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:  1.26 (0.31), residues: 836
  helix:  1.97 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.82 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 386 
 HIS   0.002   0.000   HIS B 376 
 PHE   0.018   0.001   PHE A 295 
 TYR   0.009   0.001   TYR B 274 
 ARG   0.006   0.000   ARG B 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.722 
Fit side-chains
REVERT: B  192 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8130 (t80)
REVERT: B  234 ILE cc_start: 0.8769 (tt) cc_final: 0.8496 (tt)
REVERT: B  278 GLU cc_start: 0.8467 (tt0) cc_final: 0.7997 (mt-10)
REVERT: B  299 PHE cc_start: 0.7720 (m-10) cc_final: 0.7502 (m-80)
REVERT: B  335 PHE cc_start: 0.8169 (m-80) cc_final: 0.7921 (m-80)
REVERT: B  435 PHE cc_start: 0.8330 (t80) cc_final: 0.8039 (t80)
REVERT: B  448 ASP cc_start: 0.8188 (p0) cc_final: 0.7959 (p0)
REVERT: B  476 MET cc_start: 0.7644 (mmt) cc_final: 0.7039 (pmm)
REVERT: A  192 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8128 (t80)
REVERT: A  234 ILE cc_start: 0.8778 (tt) cc_final: 0.8489 (tt)
REVERT: A  247 GLU cc_start: 0.7936 (pm20) cc_final: 0.7574 (pm20)
REVERT: A  278 GLU cc_start: 0.8491 (tt0) cc_final: 0.7995 (mt-10)
REVERT: A  299 PHE cc_start: 0.7907 (m-80) cc_final: 0.7626 (m-80)
REVERT: A  335 PHE cc_start: 0.8472 (m-80) cc_final: 0.8189 (m-80)
REVERT: A  382 PHE cc_start: 0.7772 (t80) cc_final: 0.7425 (t80)
REVERT: A  448 ASP cc_start: 0.8243 (p0) cc_final: 0.7992 (p0)
REVERT: A  476 MET cc_start: 0.7682 (mmt) cc_final: 0.7048 (pmm)
  outliers start: 21
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1378
  time to fit residues: 29.1960
Evaluate side-chains
  152 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain B residue  385 MET
Chi-restraints excluded: chain B residue  391 GLU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  457 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
A 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.120677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.104073 restraints weight = 8714.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.82
r_work: 0.3070 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6892  Z= 0.278
  Angle     :  0.596   8.198   9350  Z= 0.313
  Chirality :  0.044   0.274   1120
  Planarity :  0.005   0.050   1122
  Dihedral  :  6.908  67.333    958
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.73 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.03 (0.30), residues: 836
  helix:  1.79 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.89 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 376 
 PHE   0.019   0.001   PHE A 295 
 TYR   0.012   0.002   TYR B 283 
 ARG   0.006   0.000   ARG B 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.903 
Fit side-chains
REVERT: B  192 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8056 (t80)
REVERT: B  278 GLU cc_start: 0.8572 (tt0) cc_final: 0.8114 (mt-10)
REVERT: B  318 PHE cc_start: 0.7983 (t80) cc_final: 0.7479 (t80)
REVERT: B  435 PHE cc_start: 0.8342 (t80) cc_final: 0.8033 (t80)
REVERT: B  448 ASP cc_start: 0.8200 (p0) cc_final: 0.7945 (p0)
REVERT: B  476 MET cc_start: 0.7756 (mmt) cc_final: 0.7084 (pmm)
REVERT: A  192 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8060 (t80)
REVERT: A  234 ILE cc_start: 0.8825 (tt) cc_final: 0.8617 (tt)
REVERT: A  247 GLU cc_start: 0.7924 (pm20) cc_final: 0.7548 (pm20)
REVERT: A  278 GLU cc_start: 0.8554 (tt0) cc_final: 0.8100 (mt-10)
REVERT: A  335 PHE cc_start: 0.8541 (m-80) cc_final: 0.8228 (m-80)
REVERT: A  448 ASP cc_start: 0.8228 (p0) cc_final: 0.7958 (p0)
REVERT: A  471 LYS cc_start: 0.8244 (tppp) cc_final: 0.7827 (tptp)
REVERT: A  476 MET cc_start: 0.7771 (mmt) cc_final: 0.7104 (pmm)
  outliers start: 23
  outliers final: 18
  residues processed: 145
  average time/residue: 0.1467
  time to fit residues: 30.8600
Evaluate side-chains
  147 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 GLN
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain B residue  385 MET
Chi-restraints excluded: chain B residue  391 GLU
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:    0.0370
   chunk 39 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 49 optimal weight:    0.4980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
A 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.123679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.107237 restraints weight = 8719.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.79
r_work: 0.3110 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6892  Z= 0.204
  Angle     :  0.592   9.164   9350  Z= 0.306
  Chirality :  0.043   0.274   1120
  Planarity :  0.005   0.049   1122
  Dihedral  :  6.589  64.876    958
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.42 %
    Favored  : 78.81 %
  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:  1.13 (0.30), residues: 836
  helix:  1.84 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.76 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 386 
 HIS   0.004   0.001   HIS B 376 
 PHE   0.017   0.001   PHE B 295 
 TYR   0.009   0.001   TYR A 274 
 ARG   0.006   0.000   ARG B 364 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.899 
Fit side-chains
REVERT: B  192 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8085 (t80)
REVERT: B  278 GLU cc_start: 0.8536 (tt0) cc_final: 0.8038 (mt-10)
REVERT: B  318 PHE cc_start: 0.7937 (t80) cc_final: 0.7459 (t80)
REVERT: B  335 PHE cc_start: 0.8322 (m-80) cc_final: 0.8085 (m-80)
REVERT: B  448 ASP cc_start: 0.8182 (p0) cc_final: 0.7941 (p0)
REVERT: B  476 MET cc_start: 0.7669 (mmt) cc_final: 0.6999 (pmm)
REVERT: A  192 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8073 (t80)
REVERT: A  234 ILE cc_start: 0.8786 (tt) cc_final: 0.8525 (tt)
REVERT: A  247 GLU cc_start: 0.7980 (pm20) cc_final: 0.7663 (pm20)
REVERT: A  278 GLU cc_start: 0.8509 (tt0) cc_final: 0.7997 (mt-10)
REVERT: A  335 PHE cc_start: 0.8388 (m-80) cc_final: 0.8062 (m-80)
REVERT: A  448 ASP cc_start: 0.8197 (p0) cc_final: 0.7953 (p0)
REVERT: A  476 MET cc_start: 0.7668 (mmt) cc_final: 0.7003 (pmm)
  outliers start: 20
  outliers final: 13
  residues processed: 139
  average time/residue: 0.1402
  time to fit residues: 28.5774
Evaluate side-chains
  142 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain B residue  385 MET
Chi-restraints excluded: chain B residue  391 GLU
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 27 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:
B 250 HIS
A 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.121294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.104698 restraints weight = 8732.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.83
r_work: 0.3081 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6892  Z= 0.251
  Angle     :  0.606   8.542   9350  Z= 0.314
  Chirality :  0.044   0.271   1120
  Planarity :  0.005   0.050   1122
  Dihedral  :  6.696  66.621    958
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 18.70 %
    Favored  : 78.81 %
  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:  1.08 (0.30), residues: 836
  helix:  1.81 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.79 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 386 
 HIS   0.004   0.001   HIS B 376 
 PHE   0.018   0.001   PHE A 295 
 TYR   0.012   0.001   TYR B 283 
 ARG   0.006   0.000   ARG B 364 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2948.74 seconds
wall clock time: 53 minutes 19.39 seconds (3199.39 seconds total)