Starting phenix.real_space_refine
on Tue Mar 11 19:54:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rto_24685/03_2025/7rto_24685.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rto_24685/03_2025/7rto_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rto_24685/03_2025/7rto_24685.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rto_24685/03_2025/7rto_24685.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rto_24685/03_2025/7rto_24685.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rto_24685/03_2025/7rto_24685.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG: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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3}
          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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 92
  Time building chain proxies: 5.04, per 1000 atoms: 0.76
  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: 1.53
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.65
  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: 1.95

  Time building geometry restraints manager: 1.86 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:             3.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.030
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.700
-------------------------------------------------------------------------------
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= 0.243
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (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
 TRP   0.023   0.003   TRP C 371 
 HIS   0.010   0.001   HIS C 385 
 PHE   0.035   0.003   PHE C 470 
 TYR   0.027   0.002   TYR A 466 
 ARG   0.009   0.001   ARG A 474 

*********************** 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  : 0.705 
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: 0.7173 (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: 0.6679 (ttm-80)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1874
  time to fit residues: 34.0770
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  : 0.715 
-------------------------------------------------------------------------------
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 74 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   chunk 22 optimal weight:    7.9990
   chunk 44 optimal weight:   40.0000
   chunk 35 optimal weight:   30.0000
   chunk 68 optimal weight:   50.0000
   chunk 26 optimal weight:   20.0000
   chunk 41 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    7.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 365 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**
** C 498 GLN ** 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 = 0.3832 r_free = 0.3832 target = 0.154093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.133238 restraints weight = 11660.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.132850 restraints weight = 12901.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130457 restraints weight = 11803.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6734  Z= 0.283
  Angle     :  0.638   7.191   9130  Z= 0.346
  Chirality :  0.044   0.183   1025
  Planarity :  0.004   0.027   1206
  Dihedral  :  4.878  40.086    954
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.98 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.30), residues: 870
  helix:  2.25 (0.23), residues: 508
  sheet: -0.07 (0.47), residues: 137
  loop : -2.15 (0.39), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 
 PHE   0.019   0.002   PHE B 378 
 TYR   0.028   0.002   TYR B 482 
 ARG   0.007   0.001   ARG A 474 

*********************** 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: 12
    poor density    : 105
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A   92 GLU cc_start: 0.7346 (tp30) cc_final: 0.7128 (tp30)
REVERT: A  488 MET cc_start: 0.7926 (tpp) cc_final: 0.7596 (tpp)
REVERT: A  490 ILE cc_start: 0.8930 (mt) cc_final: 0.8708 (mt)
REVERT: B  108 ASN cc_start: 0.7658 (m110) cc_final: 0.7372 (m-40)
REVERT: B  125 LYS cc_start: 0.3608 (mtpp) cc_final: 0.3140 (mtpp)
REVERT: B  132 ASN cc_start: 0.6662 (t0) cc_final: 0.6187 (t0)
REVERT: B  467 ASP cc_start: 0.6565 (m-30) cc_final: 0.5799 (p0)
REVERT: C  114 LYS cc_start: 0.2604 (tttp) cc_final: 0.2202 (tttm)
REVERT: C  427 GLU cc_start: 0.7966 (pt0) cc_final: 0.7730 (pt0)
  outliers start: 12
  outliers final: 10
  residues processed: 113
  average time/residue: 0.1657
  time to fit residues: 25.9593
Evaluate side-chains
  100 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
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  376 VAL
Chi-restraints excluded: chain A residue  424 THR
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 73 optimal weight:    9.9990
   chunk 25 optimal weight:    0.6980
   chunk 38 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   chunk 70 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 85 optimal weight:    0.7980
   overall best weight:    4.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 496 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 = 0.3843 r_free = 0.3843 target = 0.154907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132532 restraints weight = 11836.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131934 restraints weight = 14610.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.132976 restraints weight = 11534.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6734  Z= 0.206
  Angle     :  0.570   6.211   9130  Z= 0.309
  Chirality :  0.042   0.165   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.369  18.551    951
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.26 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.30), residues: 870
  helix:  2.46 (0.23), residues: 503
  sheet:  0.13 (0.49), residues: 128
  loop : -2.33 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.020   0.002   TYR B 482 
 ARG   0.005   0.000   ARG A 474 

*********************** 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
  119 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A  360 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6769 (tm-30)
REVERT: A  445 MET cc_start: 0.8058 (tmm) cc_final: 0.7724 (tmm)
REVERT: A  488 MET cc_start: 0.8091 (tpp) cc_final: 0.7814 (tpp)
REVERT: B  108 ASN cc_start: 0.7693 (m110) cc_final: 0.7448 (m110)
REVERT: B  109 GLU cc_start: 0.5600 (tp30) cc_final: 0.5363 (tp30)
REVERT: B  132 ASN cc_start: 0.6158 (t0) cc_final: 0.5876 (t0)
REVERT: B  467 ASP cc_start: 0.6473 (m-30) cc_final: 0.5791 (p0)
REVERT: C  114 LYS cc_start: 0.2808 (tttp) cc_final: 0.2311 (tttm)
REVERT: C  118 LYS cc_start: 0.5241 (pttp) cc_final: 0.4309 (pttp)
  outliers start: 14
  outliers final: 11
  residues processed: 112
  average time/residue: 0.1670
  time to fit residues: 25.8847
Evaluate side-chains
  107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  185 HIS
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 0 optimal weight:   40.0000
   chunk 84 optimal weight:    7.9990
   chunk 69 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 6 optimal weight:   50.0000
   chunk 23 optimal weight:    0.0000
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:   30.0000
   chunk 38 optimal weight:    9.9990
   overall best weight:    3.9992

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

Flipped N/Q/H residues before XYZ refinement:
A 446 HIS
** 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 = 0.3851 r_free = 0.3851 target = 0.155587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.133346 restraints weight = 11840.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.132709 restraints weight = 12239.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.133208 restraints weight = 10249.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6734  Z= 0.185
  Angle     :  0.551   7.238   9130  Z= 0.298
  Chirality :  0.041   0.152   1025
  Planarity :  0.003   0.039   1206
  Dihedral  :  4.207  18.034    951
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.30), residues: 870
  helix:  2.46 (0.23), residues: 512
  sheet:  0.19 (0.49), residues: 128
  loop : -2.31 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 411 
 HIS   0.009   0.001   HIS B 385 
 PHE   0.017   0.002   PHE B 378 
 TYR   0.018   0.002   TYR B 482 
 ARG   0.007   0.000   ARG B 430 

*********************** 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
  114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8467 (mp) cc_final: 0.8120 (mp)
REVERT: A  360 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7069 (tm-30)
REVERT: A  488 MET cc_start: 0.8081 (tpp) cc_final: 0.7803 (tpp)
REVERT: B  108 ASN cc_start: 0.7707 (m110) cc_final: 0.7506 (m110)
REVERT: B  109 GLU cc_start: 0.5597 (tp30) cc_final: 0.5389 (tp30)
REVERT: B  132 ASN cc_start: 0.6387 (t0) cc_final: 0.5986 (t0)
REVERT: B  467 ASP cc_start: 0.6750 (m-30) cc_final: 0.5951 (p0)
REVERT: C  114 LYS cc_start: 0.2751 (tttp) cc_final: 0.2249 (tttm)
REVERT: C  118 LYS cc_start: 0.5250 (pttp) cc_final: 0.4315 (pttp)
REVERT: C  364 ILE cc_start: 0.9162 (mm) cc_final: 0.8853 (mm)
  outliers start: 15
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1737
  time to fit residues: 25.9470
Evaluate side-chains
  102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
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  360 GLN
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  185 HIS
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  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 70 optimal weight:    0.0770
   chunk 43 optimal weight:   30.0000
   chunk 48 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   overall best weight:    3.4146

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.155519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.132884 restraints weight = 11790.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.131890 restraints weight = 14068.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.133193 restraints weight = 11841.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2601

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= 0.171
  Angle     :  0.538   6.802   9130  Z= 0.290
  Chirality :  0.040   0.149   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.089  17.184    951
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.20 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.30), residues: 870
  helix:  2.60 (0.23), residues: 512
  sheet:  0.11 (0.48), residues: 137
  loop : -2.18 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 411 
 HIS   0.009   0.001   HIS B 385 
 PHE   0.017   0.002   PHE B 391 
 TYR   0.018   0.001   TYR B 482 
 ARG   0.005   0.000   ARG B 430 

*********************** 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
  122 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8424 (mp) cc_final: 0.8091 (mp)
REVERT: A  360 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7108 (tm-30)
REVERT: B  109 GLU cc_start: 0.5544 (tp30) cc_final: 0.5333 (tp30)
REVERT: B  132 ASN cc_start: 0.6334 (t0) cc_final: 0.5956 (t0)
REVERT: B  407 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7416 (pp)
REVERT: B  467 ASP cc_start: 0.6595 (m-30) cc_final: 0.5974 (p0)
REVERT: C  114 LYS cc_start: 0.2781 (tttp) cc_final: 0.2390 (tttm)
REVERT: C  118 LYS cc_start: 0.5233 (pttp) cc_final: 0.4325 (pttp)
REVERT: C  364 ILE cc_start: 0.9106 (mm) cc_final: 0.8745 (mm)
  outliers start: 18
  outliers final: 14
  residues processed: 115
  average time/residue: 0.1494
  time to fit residues: 24.5021
Evaluate side-chains
  112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
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  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  185 HIS
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  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 8 optimal weight:   30.0000
   chunk 74 optimal weight:    8.9990
   chunk 67 optimal weight:   30.0000
   chunk 59 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 44 optimal weight:    8.9990
   chunk 34 optimal weight:   50.0000
   chunk 84 optimal weight:   20.0000
   chunk 58 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0970
   overall best weight:    5.4186

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.154588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131789 restraints weight = 11746.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.130398 restraints weight = 16339.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.132040 restraints weight = 12751.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2805

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= 0.226
  Angle     :  0.572   6.516   9130  Z= 0.308
  Chirality :  0.041   0.167   1025
  Planarity :  0.003   0.026   1206
  Dihedral  :  4.244  18.656    951
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.51 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.30), residues: 870
  helix:  2.50 (0.23), residues: 512
  sheet:  0.02 (0.48), residues: 137
  loop : -2.15 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.022   0.002   TYR B 482 
 ARG   0.005   0.000   ARG B 430 

*********************** 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
  114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8348 (mp) cc_final: 0.8122 (mp)
REVERT: A  360 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.6970 (tm-30)
REVERT: A  478 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8256 (mm-40)
REVERT: B   84 ILE cc_start: 0.9461 (mm) cc_final: 0.9160 (tt)
REVERT: B  132 ASN cc_start: 0.6371 (t0) cc_final: 0.5678 (t0)
REVERT: C  114 LYS cc_start: 0.2837 (tttp) cc_final: 0.2554 (tttm)
REVERT: C  118 LYS cc_start: 0.5385 (pttp) cc_final: 0.4546 (mmmt)
REVERT: C  364 ILE cc_start: 0.9097 (mm) cc_final: 0.8735 (mm)
  outliers start: 20
  outliers final: 17
  residues processed: 108
  average time/residue: 0.1475
  time to fit residues: 22.9276
Evaluate side-chains
  102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  185 HIS
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  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 44 optimal weight:   50.0000
   chunk 2 optimal weight:    0.0040
   chunk 18 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 69 optimal weight:   30.0000
   chunk 60 optimal weight:   10.0000
   chunk 71 optimal weight:   40.0000
   overall best weight:    5.2000

-------------------------------------------------------------------------------
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 = 0.3829 r_free = 0.3829 target = 0.153718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.131952 restraints weight = 11734.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130552 restraints weight = 13468.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.131935 restraints weight = 10412.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2925

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= 0.218
  Angle     :  0.574   7.739   9130  Z= 0.308
  Chirality :  0.041   0.166   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.272  18.479    951
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.80 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.30), residues: 870
  helix:  2.47 (0.23), residues: 511
  sheet: -0.15 (0.47), residues: 139
  loop : -2.20 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 411 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.021   0.002   TYR B 482 
 ARG   0.004   0.000   ARG B 430 

*********************** 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
  114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8321 (mp) cc_final: 0.8087 (mp)
REVERT: A  360 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6767 (tm-30)
REVERT: A  478 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8604 (mm-40)
REVERT: B  132 ASN cc_start: 0.6297 (t0) cc_final: 0.5549 (t0)
REVERT: C  118 LYS cc_start: 0.4947 (pttp) cc_final: 0.4217 (mmmt)
REVERT: C  364 ILE cc_start: 0.9090 (mm) cc_final: 0.8708 (mm)
  outliers start: 21
  outliers final: 18
  residues processed: 107
  average time/residue: 0.1479
  time to fit residues: 22.9139
Evaluate side-chains
  107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
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  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  185 HIS
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  419 THR
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  427 GLU
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 65 optimal weight:   20.0000
   chunk 11 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 55 optimal weight:    8.9990
   chunk 6 optimal weight:   50.0000
   chunk 4 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0970
   chunk 75 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    5.8186

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.153018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132351 restraints weight = 11992.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131951 restraints weight = 13892.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132382 restraints weight = 11130.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.3070

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= 0.239
  Angle     :  0.595   8.550   9130  Z= 0.317
  Chirality :  0.042   0.199   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.356  18.929    951
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.80 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.30), residues: 870
  helix:  2.38 (0.22), residues: 513
  sheet: -0.24 (0.47), residues: 139
  loop : -2.22 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 371 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.023   0.002   TYR B 482 
 ARG   0.004   0.000   ARG B 430 

*********************** 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
  107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8289 (mp) cc_final: 0.8071 (mp)
REVERT: A  360 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6757 (tm-30)
REVERT: A  478 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8602 (mm-40)
REVERT: B  132 ASN cc_start: 0.6332 (t0) cc_final: 0.5569 (t0)
REVERT: C  118 LYS cc_start: 0.4972 (pttp) cc_final: 0.4259 (mmmt)
REVERT: C  364 ILE cc_start: 0.9075 (mm) cc_final: 0.8687 (mm)
  outliers start: 20
  outliers final: 16
  residues processed: 102
  average time/residue: 0.1539
  time to fit residues: 22.4598
Evaluate side-chains
  103 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
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  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
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  424 THR
Chi-restraints excluded: chain C residue  427 GLU
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 2 optimal weight:   10.0000
   chunk 50 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 56 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0770
   chunk 66 optimal weight:   20.0000
   chunk 87 optimal weight:    5.9990
   overall best weight:    5.0146

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

Flipped N/Q/H residues before XYZ refinement:
A 489 HIS
** 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 = 0.3821 r_free = 0.3821 target = 0.153359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.130361 restraints weight = 11979.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.128609 restraints weight = 9841.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.129120 restraints weight = 10267.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3111

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= 0.214
  Angle     :  0.592   9.151   9130  Z= 0.314
  Chirality :  0.042   0.181   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.325  18.286    951
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.97 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.30), residues: 870
  helix:  2.43 (0.22), residues: 511
  sheet: -0.27 (0.47), residues: 139
  loop : -2.24 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 371 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.017   0.002   PHE B 378 
 TYR   0.020   0.002   TYR B 482 
 ARG   0.004   0.000   ARG B 430 

*********************** 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
  111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7962 (mp)
REVERT: A  360 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6893 (tm-30)
REVERT: A  410 HIS cc_start: 0.7643 (m-70) cc_final: 0.7436 (m-70)
REVERT: A  478 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8348 (mm-40)
REVERT: B  132 ASN cc_start: 0.6503 (t0) cc_final: 0.5645 (t0)
REVERT: C  118 LYS cc_start: 0.4455 (pttp) cc_final: 0.3892 (mmmt)
REVERT: C  364 ILE cc_start: 0.9086 (mm) cc_final: 0.8683 (mm)
  outliers start: 19
  outliers final: 16
  residues processed: 105
  average time/residue: 0.1561
  time to fit residues: 23.5861
Evaluate side-chains
  112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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  356 ILE
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
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  424 THR
Chi-restraints excluded: chain C residue  427 GLU
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 86 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 77 optimal weight:   30.0000
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 45 optimal weight:   30.0000
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.152414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132280 restraints weight = 12147.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132384 restraints weight = 13898.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.132590 restraints weight = 10733.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6734  Z= 0.245
  Angle     :  0.615   9.661   9130  Z= 0.326
  Chirality :  0.042   0.177   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.431  18.957    951
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.97 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.30), residues: 870
  helix:  2.34 (0.22), residues: 511
  sheet: -0.37 (0.46), residues: 139
  loop : -2.28 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 411 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.023   0.002   TYR B 482 
 ARG   0.004   0.000   ARG B 430 

********************** 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  : 0.808 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7974 (mp)
REVERT: A  360 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6876 (tm-30)
REVERT: A  478 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.7913 (mp10)
REVERT: B   84 ILE cc_start: 0.9453 (mm) cc_final: 0.9096 (tt)
REVERT: B  132 ASN cc_start: 0.6125 (t0) cc_final: 0.5458 (t0)
REVERT: C  118 LYS cc_start: 0.4945 (pttp) cc_final: 0.4165 (mmmt)
REVERT: C  364 ILE cc_start: 0.9065 (mm) cc_final: 0.8675 (mm)
  outliers start: 21
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1544
  time to fit residues: 23.2452
Evaluate side-chains
  106 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
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  356 ILE
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
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   95 ILE
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  389 GLU
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  427 GLU
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 37 optimal weight:    0.5980
   chunk 42 optimal weight:   20.0000
   chunk 78 optimal weight:    8.9990
   chunk 71 optimal weight:    0.0570
   chunk 35 optimal weight:   10.0000
   chunk 69 optimal weight:   30.0000
   chunk 81 optimal weight:   20.0000
   chunk 12 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 52 optimal weight:    0.7980
   chunk 45 optimal weight:   40.0000
   overall best weight:    2.2902

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

Flipped N/Q/H residues before XYZ refinement:
B 386 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.156195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.135145 restraints weight = 11910.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.134767 restraints weight = 13255.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.133794 restraints weight = 9691.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6734  Z= 0.154
  Angle     :  0.574  10.054   9130  Z= 0.303
  Chirality :  0.041   0.179   1025
  Planarity :  0.003   0.021   1206
  Dihedral  :  4.171  17.242    951
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 22.62 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.30), residues: 870
  helix:  2.53 (0.23), residues: 509
  sheet: -0.24 (0.47), residues: 145
  loop : -2.26 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 411 
 HIS   0.009   0.001   HIS A 385 
 PHE   0.016   0.002   PHE B 391 
 TYR   0.019   0.001   TYR A  65 
 ARG   0.004   0.000   ARG B 430 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1904.33 seconds
wall clock time: 33 minutes 50.33 seconds (2030.33 seconds total)