Starting phenix.real_space_refine
on Tue Mar  3 15:26:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rto_24685/03_2026/7rto_24685.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rto_24685/03_2026/7rto_24685.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rto_24685/03_2026/7rto_24685.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rto_24685/03_2026/7rto_24685.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rto_24685/03_2026/7rto_24685.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rto_24685/03_2026/7rto_24685.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.009
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      14      5.16       5
     C    4160      2.51       5
     N    1205      2.21       5
     O    1228      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6607
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2006
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 10, 'TRANS': 259}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 189
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 164
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLU:plan': 9, 'PHE:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 92
    Chain: "B"
      Number of atoms: 2595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2595
          Classifications: {'peptide': 348}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PTRANS': 10, 'TRANS': 337}
          Chain breaks: 4
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 216
          Unresolved non-hydrogen angles: 270
          Unresolved non-hydrogen dihedrals: 180
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 7, 'GLN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 116
    Chain: "C"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2006
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 10, 'TRANS': 259}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 189
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 164
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLU:plan': 9, 'PHE:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 92
  Time building chain proxies: 1.60, per 1000 atoms: 0.24
  Number of scatterers: 6607
  At special positions: 0
  Unit cell: (104.72, 110.16, 114.24, 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      14     16.00
     O    1228      8.00
     N    1205      7.00
     C    4160      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: 0.67
  Conformation dependent library (CDL) restraints added in 238.4 milliseconds
  

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      61.3% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 80
      removed outlier: 3.716A  pdb=" N   SER A  68 " --> pdb=" O   SER A  64 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   SER A  80 " --> pdb=" O   ASN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 135
      removed outlier: 3.558A  pdb=" N   ARG A  93 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 340
      Proline residue:  A 326  - end of helix
    Processing helix  chain 'A' and resid 346 through 353
      removed outlier: 3.820A  pdb=" N   VAL A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 438
    Processing helix  chain 'A' and resid 445 through 455
      removed outlier: 3.575A  pdb=" N   ARG A 449 " --> pdb=" O   MET A 445 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   THR A 455 " --> pdb=" O   VAL A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 483
    Processing helix  chain 'A' and resid 483 through 491
      removed outlier: 3.724A  pdb=" N   GLN A 487 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 509
    Processing helix  chain 'B' and resid 65 through 79
    Processing helix  chain 'B' and resid 89 through 115
      removed outlier: 4.241A  pdb=" N   TYR B 115 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 135
      removed outlier: 7.576A  pdb=" N   LYS B 125 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   GLU B 126 " --> pdb=" O   LYS B 122 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU B 127 " --> pdb=" O   PHE B 123 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   VAL B 130 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 177
    Processing helix  chain 'B' and resid 184 through 204
    Processing helix  chain 'B' and resid 249 through 256
      removed outlier: 3.902A  pdb=" N   GLU B 253 " --> pdb=" O   GLY B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 263
    Processing helix  chain 'B' and resid 296 through 330
      Proline residue:  B 326  - end of helix
    Processing helix  chain 'B' and resid 424 through 438
    Processing helix  chain 'B' and resid 445 through 454
    Processing helix  chain 'B' and resid 469 through 482
    Processing helix  chain 'B' and resid 483 through 491
      removed outlier: 3.572A  pdb=" N   GLN B 487 " --> pdb=" O   ASP B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 509
    Processing helix  chain 'B' and resid 510 through 513
    Processing helix  chain 'C' and resid 65 through 79
    Processing helix  chain 'C' and resid 89 through 135
      removed outlier: 4.531A  pdb=" N   ASN C 135 " --> pdb=" O   TYR C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 340
      Proline residue:  C 326  - end of helix
      removed outlier: 4.211A  pdb=" N   GLY C 340 " --> pdb=" O   LYS C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 343
      No H-bonds generated for 'chain 'C' and resid 341 through 343'
    Processing helix  chain 'C' and resid 346 through 351
    Processing helix  chain 'C' and resid 424 through 438
      removed outlier: 3.524A  pdb=" N   SER C 438 " --> pdb=" O   ASN C 434 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 454
    Processing helix  chain 'C' and resid 469 through 483
    Processing helix  chain 'C' and resid 484 through 491
      removed outlier: 3.786A  pdb=" N   HIS C 489 " --> pdb=" O   GLU C 485 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 494 through 509
    Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 406
      removed outlier: 3.721A  pdb=" N   GLY A 462 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   SER A 368 " --> pdb=" O   TYR A 460 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   TYR A 460 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 414
    Processing sheet with id=AA3, first strand: chain 'B' and resid 401 through 408
      removed outlier: 3.884A  pdb=" N   GLY B 462 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   SER B 368 " --> pdb=" O   TYR B 460 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   TYR B 460 " --> pdb=" O   SER B 368 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 412 through 414
    Processing sheet with id=AA5, first strand: chain 'C' and resid 401 through 406
      removed outlier: 4.085A  pdb=" N   GLY C 462 " --> pdb=" O   VAL C 366 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   SER C 368 " --> pdb=" O   TYR C 460 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   TYR C 460 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 414

    468 hydrogen bonds defined for protein.
    1362 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 0.82 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: 2122
        1.34 -     1.45: 955
        1.45 -     1.57: 3635
        1.57 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 6734
  Sorted by residual:
  bond pdb=" N   GLN A 360 "
       pdb=" CA  GLN A 360 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.034 1.33e-02 5.65e+03 6.65e+00
  bond pdb=" N   ASP A 406 "
       pdb=" CA  ASP A 406 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.31e-02 5.83e+03 6.35e+00
  bond pdb=" N   LEU C 113 "
       pdb=" CA  LEU C 113 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.19e-02 7.06e+03 5.52e+00
  bond pdb=" CG1 ILE C 490 "
       pdb=" CD1 ILE C 490 "
    ideal  model  delta    sigma   weight residual
    1.513  1.451  0.062 3.90e-02 6.57e+02 2.50e+00
  bond pdb=" CB  GLN C 361 "
       pdb=" CG  GLN C 361 "
    ideal  model  delta    sigma   weight residual
    1.520  1.478  0.042 3.00e-02 1.11e+03 1.94e+00
  ... (remaining 6729 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 8754
        1.90 -     3.79: 315
        3.79 -     5.69: 47
        5.69 -     7.59: 6
        7.59 -     9.48: 8
  Bond angle restraints: 9130
  Sorted by residual:
  angle pdb=" O   GLN A 360 "
        pdb=" C   GLN A 360 "
        pdb=" N   GLN A 361 "
      ideal   model   delta    sigma   weight residual
     122.18  125.88   -3.70 9.90e-01 1.02e+00 1.39e+01
  angle pdb=" CB  LYS A 511 "
        pdb=" CG  LYS A 511 "
        pdb=" CD  LYS A 511 "
      ideal   model   delta    sigma   weight residual
     111.30  119.34   -8.04 2.30e+00 1.89e-01 1.22e+01
  angle pdb=" CG1 ILE C 356 "
        pdb=" CB  ILE C 356 "
        pdb=" CG2 ILE C 356 "
      ideal   model   delta    sigma   weight residual
     110.70  101.37    9.33 3.00e+00 1.11e-01 9.68e+00
  angle pdb=" CA  GLN C 478 "
        pdb=" CB  GLN C 478 "
        pdb=" CG  GLN C 478 "
      ideal   model   delta    sigma   weight residual
     114.10  120.15   -6.05 2.00e+00 2.50e-01 9.16e+00
  angle pdb=" C   ALA C 359 "
        pdb=" N   GLN C 360 "
        pdb=" CA  GLN C 360 "
      ideal   model   delta    sigma   weight residual
     122.23  126.83   -4.60 1.57e+00 4.06e-01 8.59e+00
  ... (remaining 9125 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3603
       17.85 -    35.69: 322
       35.69 -    53.53: 58
       53.53 -    71.38: 9
       71.38 -    89.22: 6
  Dihedral angle restraints: 3998
    sinusoidal: 1429
      harmonic: 2569
  Sorted by residual:
  dihedral pdb=" CA  TYR C  65 "
           pdb=" C   TYR C  65 "
           pdb=" N   GLY C  66 "
           pdb=" CA  GLY C  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.44  -22.56     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  HIS A 385 "
           pdb=" C   HIS A 385 "
           pdb=" N   HIS A 386 "
           pdb=" CA  HIS A 386 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.58   22.42     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  TYR B 404 "
           pdb=" C   TYR B 404 "
           pdb=" N   GLU B 405 "
           pdb=" CA  GLU B 405 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.48   20.52     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 3995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 955
       0.090 -    0.179: 61
       0.179 -    0.269: 8
       0.269 -    0.359: 0
       0.359 -    0.448: 1
  Chirality restraints: 1025
  Sorted by residual:
  chirality pdb=" CB  ILE A 356 "
            pdb=" CA  ILE A 356 "
            pdb=" CG1 ILE A 356 "
            pdb=" CG2 ILE A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.45 2.00e-01 2.50e+01 5.02e+00
  chirality pdb=" CB  ILE C 356 "
            pdb=" CA  ILE C 356 "
            pdb=" CG1 ILE C 356 "
            pdb=" CG2 ILE C 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  ILE C 364 "
            pdb=" N   ILE C 364 "
            pdb=" C   ILE C 364 "
            pdb=" CB  ILE C 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1022 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 448 "    0.023 2.00e-02 2.50e+03   4.55e-02 2.07e+01
        pdb=" C   ARG A 448 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   ARG A 448 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ARG A 449 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 466 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.98e+00
        pdb=" C   TYR C 466 "    0.046 2.00e-02 2.50e+03
        pdb=" O   TYR C 466 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP C 467 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 477 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.58e+00
        pdb=" C   ALA C 477 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ALA C 477 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLN C 478 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 537
        2.74 -     3.28: 6560
        3.28 -     3.82: 10786
        3.82 -     4.36: 11393
        4.36 -     4.90: 20404
  Nonbonded interactions: 49680
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 493 "
            pdb=" NE2 GLN A 498 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" O   LEU A 450 "
            pdb=" OG  SER A 453 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   HIS A 384 "
            pdb=" ND1 HIS A 385 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" O   ALA A 369 "
            pdb=" OG  SER A 373 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   SER C  89 "
            pdb=" OG  SER C  89 "
     model   vdw
     2.385 3.040
  ... (remaining 49675 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}

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:             2.150
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.140
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
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   6734  Z= 0.174
  Angle     :  0.821   9.484   9130  Z= 0.449
  Chirality :  0.052   0.448   1025
  Planarity :  0.005   0.045   1206
  Dihedral  : 14.320  89.223   2334
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.00 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.30), residues: 870
  helix:  2.41 (0.23), residues: 490
  sheet: -0.19 (0.49), residues: 124
  loop : -2.30 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 474 
 TYR   0.027   0.002   TYR A 466 
 PHE   0.035   0.003   PHE C 470 
 TRP   0.023   0.003   TRP C 371 
 HIS   0.010   0.001   HIS C 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6734)
  covalent geometry    : angle       0.82120 ( 9130)
  hydrogen bonds       : bond        0.09952 (  468)
  hydrogen bonds       : angle       5.48621 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  360 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6531 (tm-30)
REVERT: A  490 ILE cc_start: 0.8918 (mt) cc_final: 0.8640 (mt)
REVERT: B  108 ASN cc_start: 0.7412 (m110) cc_final: 0.7172 (m110)
REVERT: B  132 ASN cc_start: 0.5924 (t0) cc_final: 0.5670 (t0)
REVERT: C  448 ARG cc_start: 0.6949 (ttm-80) cc_final: 0.6678 (ttm-80)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0889
  time to fit residues: 16.2249
Evaluate side-chains
  94 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:   40.0000
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
A 446 HIS
A 478 GLN
B 177 GLN
** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.158706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.136479 restraints weight = 11850.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.134745 restraints weight = 14729.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.136240 restraints weight = 11618.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.136240 restraints weight = 8008.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.136299 restraints weight = 7063.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6734  Z= 0.124
  Angle     :  0.577   6.585   9130  Z= 0.312
  Chirality :  0.042   0.185   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.470  33.136    954
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.00 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.30), residues: 870
  helix:  2.49 (0.23), residues: 507
  sheet:  0.21 (0.49), residues: 128
  loop : -2.21 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 474 
 TYR   0.021   0.002   TYR B 482 
 PHE   0.019   0.002   PHE C 378 
 TRP   0.011   0.002   TRP C 411 
 HIS   0.009   0.001   HIS C 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6734)
  covalent geometry    : angle       0.57746 ( 9130)
  hydrogen bonds       : bond        0.03776 (  468)
  hydrogen bonds       : angle       4.32116 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  488 MET cc_start: 0.8017 (tpp) cc_final: 0.7786 (tpp)
REVERT: B  108 ASN cc_start: 0.7293 (m110) cc_final: 0.6845 (m-40)
REVERT: B  132 ASN cc_start: 0.6159 (t0) cc_final: 0.5854 (t0)
REVERT: B  467 ASP cc_start: 0.6037 (m-30) cc_final: 0.5501 (p0)
REVERT: C  374 ASP cc_start: 0.7760 (p0) cc_final: 0.7240 (p0)
  outliers start: 9
  outliers final: 7
  residues processed: 114
  average time/residue: 0.0732
  time to fit residues: 11.7359
Evaluate side-chains
  99 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 52 optimal weight:    7.9990
   chunk 71 optimal weight:    0.0050
   chunk 4 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 54 optimal weight:   30.0000
   chunk 35 optimal weight:   20.0000
   chunk 36 optimal weight:    4.9990
   chunk 10 optimal weight:   50.0000
   overall best weight:    5.4002

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

Flipped N/Q/H residues before XYZ refinement:
A 365 HIS
A 498 GLN
** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 386 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 = 0.3834 r_free = 0.3834 target = 0.154118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.132068 restraints weight = 11799.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.131465 restraints weight = 14314.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.131400 restraints weight = 13224.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132546 restraints weight = 8945.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132508 restraints weight = 7258.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6734  Z= 0.149
  Angle     :  0.586   7.127   9130  Z= 0.316
  Chirality :  0.042   0.163   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.352  19.214    951
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.26 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.30), residues: 870
  helix:  2.54 (0.23), residues: 503
  sheet:  0.10 (0.48), residues: 137
  loop : -2.26 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 474 
 TYR   0.023   0.002   TYR B 482 
 PHE   0.017   0.002   PHE B 391 
 TRP   0.016   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6734)
  covalent geometry    : angle       0.58586 ( 9130)
  hydrogen bonds       : bond        0.03925 (  468)
  hydrogen bonds       : angle       4.25247 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8441 (mp) cc_final: 0.8174 (mp)
REVERT: A  360 GLN cc_start: 0.7373 (tt0) cc_final: 0.6874 (tm-30)
REVERT: A  445 MET cc_start: 0.7904 (tmm) cc_final: 0.7582 (tmm)
REVERT: A  488 MET cc_start: 0.8104 (tpp) cc_final: 0.7817 (tpp)
REVERT: B  108 ASN cc_start: 0.7668 (m110) cc_final: 0.7407 (m110)
REVERT: B  132 ASN cc_start: 0.6299 (t0) cc_final: 0.5968 (t0)
REVERT: B  467 ASP cc_start: 0.6514 (m-30) cc_final: 0.5890 (p0)
REVERT: C  114 LYS cc_start: 0.2606 (tttp) cc_final: 0.2221 (tttm)
REVERT: C  364 ILE cc_start: 0.9157 (mm) cc_final: 0.8792 (mm)
  outliers start: 12
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0747
  time to fit residues: 11.5429
Evaluate side-chains
  105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  451 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 12 optimal weight:   20.0000
   chunk 71 optimal weight:    0.0570
   chunk 59 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 70 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    3.0106

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

Flipped N/Q/H residues before XYZ refinement:
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.155634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.133415 restraints weight = 11910.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.133069 restraints weight = 13252.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.133591 restraints weight = 10708.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.133668 restraints weight = 8284.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.133778 restraints weight = 6876.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6734  Z= 0.110
  Angle     :  0.528   6.067   9130  Z= 0.286
  Chirality :  0.040   0.154   1025
  Planarity :  0.003   0.020   1206
  Dihedral  :  4.093  17.134    951
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.56 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.30), residues: 870
  helix:  2.63 (0.23), residues: 508
  sheet:  0.23 (0.50), residues: 128
  loop : -2.37 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 474 
 TYR   0.016   0.001   TYR B 482 
 PHE   0.017   0.002   PHE B 391 
 TRP   0.010   0.001   TRP C 411 
 HIS   0.009   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6734)
  covalent geometry    : angle       0.52763 ( 9130)
  hydrogen bonds       : bond        0.03436 (  468)
  hydrogen bonds       : angle       4.01762 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8442 (mp) cc_final: 0.8216 (mp)
REVERT: A  360 GLN cc_start: 0.7355 (tt0) cc_final: 0.6918 (tm-30)
REVERT: A  488 MET cc_start: 0.8089 (tpp) cc_final: 0.7819 (tpp)
REVERT: B  132 ASN cc_start: 0.6340 (t0) cc_final: 0.5967 (t0)
REVERT: B  467 ASP cc_start: 0.6532 (m-30) cc_final: 0.5935 (p0)
REVERT: C  114 LYS cc_start: 0.2560 (tttp) cc_final: 0.2166 (tttm)
REVERT: C  364 ILE cc_start: 0.9140 (mm) cc_final: 0.8784 (mm)
REVERT: C  427 GLU cc_start: 0.7665 (pt0) cc_final: 0.7439 (pt0)
  outliers start: 12
  outliers final: 10
  residues processed: 116
  average time/residue: 0.0753
  time to fit residues: 12.2061
Evaluate side-chains
  104 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:   30.0000
   chunk 78 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 23 optimal weight:   20.0000
   chunk 83 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0270
   chunk 59 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 52 optimal weight:   20.0000
   chunk 84 optimal weight:    5.9990
   overall best weight:    4.4044

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

Flipped N/Q/H residues before XYZ refinement:
B 108 ASN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.155107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.132337 restraints weight = 11935.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.131585 restraints weight = 14409.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.132395 restraints weight = 11911.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.132699 restraints weight = 8545.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.132876 restraints weight = 7546.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6734  Z= 0.131
  Angle     :  0.558   7.477   9130  Z= 0.299
  Chirality :  0.041   0.151   1025
  Planarity :  0.003   0.021   1206
  Dihedral  :  4.144  17.718    951
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.38 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.30), residues: 870
  helix:  2.58 (0.23), residues: 510
  sheet:  0.09 (0.48), residues: 137
  loop : -2.19 (0.40), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 474 
 TYR   0.020   0.001   TYR B 482 
 PHE   0.017   0.002   PHE B 378 
 TRP   0.011   0.001   TRP C 411 
 HIS   0.009   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6734)
  covalent geometry    : angle       0.55827 ( 9130)
  hydrogen bonds       : bond        0.03589 (  468)
  hydrogen bonds       : angle       4.05841 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8405 (mp) cc_final: 0.8167 (mp)
REVERT: A  360 GLN cc_start: 0.7643 (tt0) cc_final: 0.7006 (tm-30)
REVERT: B   84 ILE cc_start: 0.9403 (mm) cc_final: 0.9135 (tt)
REVERT: B  132 ASN cc_start: 0.6333 (t0) cc_final: 0.5974 (t0)
REVERT: B  467 ASP cc_start: 0.6668 (m-30) cc_final: 0.6021 (p0)
REVERT: C  114 LYS cc_start: 0.2764 (tttp) cc_final: 0.2316 (tttm)
REVERT: C  118 LYS cc_start: 0.5327 (pttp) cc_final: 0.4372 (pttp)
REVERT: C  364 ILE cc_start: 0.9109 (mm) cc_final: 0.8746 (mm)
  outliers start: 16
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0672
  time to fit residues: 10.3056
Evaluate side-chains
  108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  443 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:   30.0000
   chunk 22 optimal weight:    0.0170
   chunk 64 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 49 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    5.8026

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

Flipped N/Q/H residues before XYZ refinement:
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.153970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131484 restraints weight = 11918.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.130789 restraints weight = 13840.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.131708 restraints weight = 11467.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.131914 restraints weight = 8595.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131989 restraints weight = 7266.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6734  Z= 0.153
  Angle     :  0.577   6.747   9130  Z= 0.311
  Chirality :  0.042   0.184   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.293  18.918    951
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.85 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.30), residues: 870
  helix:  2.46 (0.23), residues: 512
  sheet: -0.11 (0.47), residues: 139
  loop : -2.15 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 474 
 TYR   0.023   0.002   TYR B 482 
 PHE   0.018   0.002   PHE B 378 
 TRP   0.013   0.002   TRP C 411 
 HIS   0.010   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6734)
  covalent geometry    : angle       0.57722 ( 9130)
  hydrogen bonds       : bond        0.03788 (  468)
  hydrogen bonds       : angle       4.16736 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  478 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8619 (mm-40)
REVERT: B  132 ASN cc_start: 0.6383 (t0) cc_final: 0.5704 (t0)
REVERT: C  114 LYS cc_start: 0.2880 (tttp) cc_final: 0.2602 (tttm)
REVERT: C  118 LYS cc_start: 0.5057 (pttp) cc_final: 0.4259 (mmmt)
REVERT: C  364 ILE cc_start: 0.9096 (mm) cc_final: 0.8734 (mm)
  outliers start: 22
  outliers final: 18
  residues processed: 107
  average time/residue: 0.0683
  time to fit residues: 10.5376
Evaluate side-chains
  105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  405 GLU
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 76 optimal weight:    0.0070
   chunk 59 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 55 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   chunk 79 optimal weight:    8.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    5.0006

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

Flipped N/Q/H residues before XYZ refinement:
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.153596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.129778 restraints weight = 11701.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.127801 restraints weight = 8946.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.128069 restraints weight = 8841.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.128224 restraints weight = 7637.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.128413 restraints weight = 7359.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6734  Z= 0.140
  Angle     :  0.572   7.633   9130  Z= 0.307
  Chirality :  0.041   0.175   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.272  18.447    951
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.51 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.30), residues: 870
  helix:  2.49 (0.23), residues: 511
  sheet: -0.13 (0.46), residues: 139
  loop : -2.18 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 474 
 TYR   0.020   0.002   TYR B 482 
 PHE   0.018   0.002   PHE B 378 
 TRP   0.011   0.002   TRP C 411 
 HIS   0.010   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6734)
  covalent geometry    : angle       0.57175 ( 9130)
  hydrogen bonds       : bond        0.03644 (  468)
  hydrogen bonds       : angle       4.14246 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  478 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8615 (mm-40)
REVERT: B   84 ILE cc_start: 0.9440 (mm) cc_final: 0.9174 (tt)
REVERT: B  132 ASN cc_start: 0.6474 (t0) cc_final: 0.5651 (t0)
REVERT: B  467 ASP cc_start: 0.6650 (m-30) cc_final: 0.6433 (p0)
REVERT: C  118 LYS cc_start: 0.4414 (pttp) cc_final: 0.3834 (mmmt)
REVERT: C  364 ILE cc_start: 0.9094 (mm) cc_final: 0.8717 (mm)
  outliers start: 22
  outliers final: 21
  residues processed: 110
  average time/residue: 0.0639
  time to fit residues: 10.1822
Evaluate side-chains
  110 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  443 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  389 GLU
Chi-restraints excluded: chain C residue  405 GLU
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 44 optimal weight:   20.0000
   chunk 58 optimal weight:   20.0000
   chunk 64 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 108 ASN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.153541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131051 restraints weight = 11947.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.129858 restraints weight = 16322.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.131166 restraints weight = 12756.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.131307 restraints weight = 8252.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131471 restraints weight = 7895.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6734  Z= 0.132
  Angle     :  0.583   8.639   9130  Z= 0.308
  Chirality :  0.041   0.172   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.234  17.977    951
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.67 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.30), residues: 870
  helix:  2.52 (0.23), residues: 511
  sheet: -0.13 (0.47), residues: 139
  loop : -2.19 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 474 
 TYR   0.019   0.002   TYR B 482 
 PHE   0.017   0.002   PHE B 378 
 TRP   0.011   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6734)
  covalent geometry    : angle       0.58322 ( 9130)
  hydrogen bonds       : bond        0.03572 (  468)
  hydrogen bonds       : angle       4.15450 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  478 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8614 (mm-40)
REVERT: B   84 ILE cc_start: 0.9420 (mm) cc_final: 0.9132 (tt)
REVERT: B  132 ASN cc_start: 0.6228 (t0) cc_final: 0.5545 (t0)
REVERT: C  118 LYS cc_start: 0.5019 (pttp) cc_final: 0.4334 (mmmt)
REVERT: C  364 ILE cc_start: 0.9074 (mm) cc_final: 0.8685 (mm)
  outliers start: 23
  outliers final: 21
  residues processed: 106
  average time/residue: 0.0670
  time to fit residues: 10.2306
Evaluate side-chains
  110 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  443 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  389 GLU
Chi-restraints excluded: chain C residue  405 GLU
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 45 optimal weight:   50.0000
   chunk 3 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 60 optimal weight:   20.0000
   chunk 75 optimal weight:    8.9990
   chunk 81 optimal weight:   20.0000
   chunk 65 optimal weight:   20.0000
   overall best weight:    6.3992

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.151996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130642 restraints weight = 12126.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.129818 restraints weight = 17198.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.130398 restraints weight = 12462.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.130231 restraints weight = 11181.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.130740 restraints weight = 9025.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6734  Z= 0.167
  Angle     :  0.618   8.975   9130  Z= 0.329
  Chirality :  0.042   0.203   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.462  19.437    951
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.33 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.30), residues: 870
  helix:  2.41 (0.22), residues: 511
  sheet: -0.29 (0.46), residues: 139
  loop : -2.29 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 474 
 TYR   0.024   0.002   TYR B 482 
 PHE   0.018   0.002   PHE B 378 
 TRP   0.014   0.002   TRP C 411 
 HIS   0.010   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6734)
  covalent geometry    : angle       0.61828 ( 9130)
  hydrogen bonds       : bond        0.03924 (  468)
  hydrogen bonds       : angle       4.29445 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  410 HIS cc_start: 0.7629 (m-70) cc_final: 0.7416 (m-70)
REVERT: A  478 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8374 (mm-40)
REVERT: B   84 ILE cc_start: 0.9433 (mm) cc_final: 0.9127 (tt)
REVERT: B  132 ASN cc_start: 0.6289 (t0) cc_final: 0.5594 (t0)
REVERT: C  118 LYS cc_start: 0.5066 (pttp) cc_final: 0.4317 (mmmt)
REVERT: C  364 ILE cc_start: 0.9083 (mm) cc_final: 0.8693 (mm)
  outliers start: 21
  outliers final: 19
  residues processed: 102
  average time/residue: 0.0671
  time to fit residues: 9.8445
Evaluate side-chains
  103 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  386 HIS
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  389 GLU
Chi-restraints excluded: chain C residue  405 GLU
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 15 optimal weight:    7.9990
   chunk 66 optimal weight:    0.7980
   chunk 67 optimal weight:    8.9990
   chunk 72 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.153693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.132621 restraints weight = 11942.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.132122 restraints weight = 12904.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.131531 restraints weight = 9886.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.131828 restraints weight = 9000.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131958 restraints weight = 7256.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6734  Z= 0.137
  Angle     :  0.599   8.846   9130  Z= 0.316
  Chirality :  0.041   0.189   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.329  18.117    951
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.33 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.30), residues: 870
  helix:  2.46 (0.23), residues: 511
  sheet: -0.26 (0.46), residues: 139
  loop : -2.26 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 474 
 TYR   0.020   0.002   TYR B 482 
 PHE   0.017   0.002   PHE B 378 
 TRP   0.012   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6734)
  covalent geometry    : angle       0.59913 ( 9130)
  hydrogen bonds       : bond        0.03724 (  468)
  hydrogen bonds       : angle       4.27512 ( 1362)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  478 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8611 (mm-40)
REVERT: B  132 ASN cc_start: 0.6260 (t0) cc_final: 0.5582 (t0)
REVERT: C  118 LYS cc_start: 0.4902 (pttp) cc_final: 0.4175 (mmmt)
REVERT: C  364 ILE cc_start: 0.9077 (mm) cc_final: 0.8684 (mm)
  outliers start: 21
  outliers final: 20
  residues processed: 106
  average time/residue: 0.0689
  time to fit residues: 10.4521
Evaluate side-chains
  108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  386 HIS
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  443 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  389 GLU
Chi-restraints excluded: chain C residue  405 GLU
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 85 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 58 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   overall best weight:    4.9188

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

Flipped N/Q/H residues before XYZ refinement:
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.153251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.132272 restraints weight = 11989.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130236 restraints weight = 10139.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.128767 restraints weight = 7973.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.129304 restraints weight = 7196.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.129580 restraints weight = 6336.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6734  Z= 0.143
  Angle     :  0.611   9.362   9130  Z= 0.323
  Chirality :  0.042   0.179   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.351  18.385    951
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.98 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.30), residues: 870
  helix:  2.43 (0.22), residues: 510
  sheet: -0.26 (0.47), residues: 139
  loop : -2.21 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 474 
 TYR   0.021   0.002   TYR B 482 
 PHE   0.018   0.002   PHE B 378 
 TRP   0.013   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6734)
  covalent geometry    : angle       0.61060 ( 9130)
  hydrogen bonds       : bond        0.03728 (  468)
  hydrogen bonds       : angle       4.27022 ( 1362)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1085.91 seconds
wall clock time: 19 minutes 25.50 seconds (1165.50 seconds total)