Starting phenix.real_space_refine
on Wed Feb 12 20:13:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k0e_36762/02_2025/8k0e_36762.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k0e_36762/02_2025/8k0e_36762.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k0e_36762/02_2025/8k0e_36762.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k0e_36762/02_2025/8k0e_36762.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k0e_36762/02_2025/8k0e_36762.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k0e_36762/02_2025/8k0e_36762.cif"
  }
  resolution = 3.65
  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=   0.005 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      47      5.16       5
     C    5273      2.51       5
     N    1403      2.21       5
     O    1576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8300
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 646, 5193
          Classifications: {'peptide': 646}
          Link IDs: {'PTRANS': 33, 'TRANS': 612}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2994
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 18, 'TRANS': 343}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' FE': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.20, per 1000 atoms: 0.63
  Number of scatterers: 8300
  At special positions: 0
  Unit cell: (81.4, 105.6, 125.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      47     16.00
     O    1576      8.00
     N    1403      7.00
     C    5273      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 242 " - pdb=" SG  CYS A 282 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 540 "
      " NAG D   1 " - " ASN A 316 "
      " NAG E   1 " - " ASN B 363 "
      " NAG F   1 " - " ASN B  87 "
  Time building additional restraints: 2.33
  Conformation dependent library (CDL) restraints added in 972.2 milliseconds
  

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1922

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 3 sheets defined
      65.2% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 49
      removed outlier: 3.746A  pdb=" N   LEU A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 83
      removed outlier: 3.814A  pdb=" N   ALA A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 125
      removed outlier: 3.692A  pdb=" N   GLY A 125 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 142
      removed outlier: 3.923A  pdb=" N   GLU A 137 " --> pdb=" O   SER A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 176 through 189
      removed outlier: 3.521A  pdb=" N   GLN A 180 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A 189 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 197
    Processing helix  chain 'A' and resid 203 through 217
      removed outlier: 3.549A  pdb=" N   GLN A 207 " --> pdb=" O   GLN A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.038A  pdb=" N   HIS A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 281
      removed outlier: 3.644A  pdb=" N   THR A 269 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 285
    Processing helix  chain 'A' and resid 298 through 315
    Processing helix  chain 'A' and resid 316 through 329
    Processing helix  chain 'A' and resid 334 through 348
    Processing helix  chain 'A' and resid 349 through 356
      removed outlier: 3.541A  pdb=" N   ILE A 356 " --> pdb=" O   HIS A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 384
    Processing helix  chain 'A' and resid 400 through 428
    Processing helix  chain 'A' and resid 441 through 447
    Processing helix  chain 'A' and resid 479 through 493
      removed outlier: 3.578A  pdb=" N   CYS A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA A 493 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 528
    Processing helix  chain 'A' and resid 531 through 553
      removed outlier: 3.862A  pdb=" N   ALA A 535 " --> pdb=" O   PRO A 531 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   PHE A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 576
      removed outlier: 3.863A  pdb=" N   GLN A 576 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 598
    Processing helix  chain 'A' and resid 686 through 699
    Processing helix  chain 'B' and resid 37 through 41
      removed outlier: 3.864A  pdb=" N   GLU B  40 " --> pdb=" O   PRO B  37 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU B  41 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 37 through 41'
    Processing helix  chain 'B' and resid 43 through 57
    Processing helix  chain 'B' and resid 60 through 90
      removed outlier: 3.776A  pdb=" N   CYS B  88 " --> pdb=" O   CYS B  84 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER B  89 " --> pdb=" O   HIS B  85 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ALA B  90 " --> pdb=" O   ARG B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 102
    Processing helix  chain 'B' and resid 103 through 123
    Processing helix  chain 'B' and resid 124 through 125
      No H-bonds generated for 'chain 'B' and resid 124 through 125'
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 4.205A  pdb=" N   GLN B 131 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 144
    Processing helix  chain 'B' and resid 146 through 157
      removed outlier: 4.200A  pdb=" N   PHE B 150 " --> pdb=" O   GLU B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 175
      removed outlier: 3.820A  pdb=" N   LYS B 174 " --> pdb=" O   THR B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 191
    Processing helix  chain 'B' and resid 204 through 219
      removed outlier: 3.729A  pdb=" N   SER B 208 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 246
      Proline residue:  B 234  - end of helix
    Processing helix  chain 'B' and resid 258 through 276
      removed outlier: 4.427A  pdb=" N   HIS B 266 " --> pdb=" O   SER B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 308
    Processing helix  chain 'B' and resid 310 through 325
      Proline residue:  B 316  - end of helix
    Processing helix  chain 'B' and resid 328 through 341
      removed outlier: 3.722A  pdb=" N   HIS B 341 " --> pdb=" O   TYR B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 352
      removed outlier: 3.827A  pdb=" N   PHE B 352 " --> pdb=" O   ASP B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 376
    Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 461
      removed outlier: 6.194A  pdb=" N   LEU A 459 " --> pdb=" O   ASP A 475 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP A 475 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ARG A 647 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 673 " --> pdb=" O   HIS A 565 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   HIS A 565 " --> pdb=" O   ALA A 673 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TYR A 563 " --> pdb=" O   TRP A 675 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   THR A 677 " --> pdb=" O   PHE A 561 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   PHE A 561 " --> pdb=" O   THR A 677 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   VAL A 516 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 584 through 587
      removed outlier: 6.223A  pdb=" N   VAL A 661 " --> pdb=" O   PRO A 585 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   HIS A 587 " --> pdb=" O   HIS A 659 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   PHE A 627 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLU A 640 " --> pdb=" O   PHE A 627 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   PHE A 629 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 284 through 285
      removed outlier: 4.194A  pdb=" N   ILE B 285 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1407 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1735
        1.33 -     1.45: 2087
        1.45 -     1.58: 4613
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 8505
  Sorted by residual:
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.479 -0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.62e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.27e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.26e+00
  ... (remaining 8500 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 11437
        3.30 -     6.60: 64
        6.60 -     9.90: 9
        9.90 -    13.20: 3
       13.20 -    16.50: 2
  Bond angle restraints: 11515
  Sorted by residual:
  angle pdb=" CA  LEU A 183 "
        pdb=" CB  LEU A 183 "
        pdb=" CG  LEU A 183 "
      ideal   model   delta    sigma   weight residual
     116.30  132.80  -16.50 3.50e+00 8.16e-02 2.22e+01
  angle pdb=" CB  MET A 177 "
        pdb=" CG  MET A 177 "
        pdb=" SD  MET A 177 "
      ideal   model   delta    sigma   weight residual
     112.70  126.80  -14.10 3.00e+00 1.11e-01 2.21e+01
  angle pdb=" CA  LEU A 445 "
        pdb=" CB  LEU A 445 "
        pdb=" CG  LEU A 445 "
      ideal   model   delta    sigma   weight residual
     116.30  129.47  -13.17 3.50e+00 8.16e-02 1.41e+01
  angle pdb=" CA  LEU A 215 "
        pdb=" CB  LEU A 215 "
        pdb=" CG  LEU A 215 "
      ideal   model   delta    sigma   weight residual
     116.30  128.23  -11.93 3.50e+00 8.16e-02 1.16e+01
  angle pdb=" N   GLY B 125 "
        pdb=" CA  GLY B 125 "
        pdb=" C   GLY B 125 "
      ideal   model   delta    sigma   weight residual
     110.21  113.23   -3.02 9.10e-01 1.21e+00 1.10e+01
  ... (remaining 11510 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.71: 4638
       24.71 -    49.42: 474
       49.42 -    74.12: 69
       74.12 -    98.83: 26
       98.83 -   123.54: 18
  Dihedral angle restraints: 5225
    sinusoidal: 2237
      harmonic: 2988
  Sorted by residual:
  dihedral pdb=" CB  CYS A  75 "
           pdb=" SG  CYS A  75 "
           pdb=" SG  CYS A 123 "
           pdb=" CB  CYS A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.25  -88.75     1      1.00e+01 1.00e-02 9.39e+01
  dihedral pdb=" CB  CYS A 242 "
           pdb=" SG  CYS A 242 "
           pdb=" SG  CYS A 282 "
           pdb=" CB  CYS A 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.78  -43.78     1      1.00e+01 1.00e-02 2.67e+01
  dihedral pdb=" C2  NAG C   1 "
           pdb=" C1  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C5  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   60.58 -123.54     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 5222 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 904
       0.041 -    0.081: 243
       0.081 -    0.122: 70
       0.122 -    0.162: 6
       0.162 -    0.203: 3
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" CG  LEU A 138 "
            pdb=" CB  LEU A 138 "
            pdb=" CD1 LEU A 138 "
            pdb=" CD2 LEU A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  MET B 331 "
            pdb=" N   MET B 331 "
            pdb=" C   MET B 331 "
            pdb=" CB  MET B 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" CB  THR A  34 "
            pdb=" CA  THR A  34 "
            pdb=" OG1 THR A  34 "
            pdb=" CG2 THR A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 6.95e-01
  ... (remaining 1223 not shown)

  Planarity restraints: 1512
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  94 "   -0.061 5.00e-02 4.00e+02   8.98e-02 1.29e+01
        pdb=" N   PRO A  95 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 604 "   -0.042 5.00e-02 4.00e+02   6.33e-02 6.41e+00
        pdb=" N   PRO A 605 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 605 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 605 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 657 "   -0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO A 658 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 658 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 658 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1509 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 125
        2.66 -     3.22: 7857
        3.22 -     3.78: 12732
        3.78 -     4.34: 15006
        4.34 -     4.90: 24964
  Nonbonded interactions: 60684
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 312 "
            pdb=" OH  TYR A 343 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" O   TYR A 185 "
            pdb=" OG1 THR A 188 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG  SER A 133 "
            pdb=" OE1 GLU A 135 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O4  NAG D   2 "
            pdb=" O7  NAG D   2 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OD2 ASP A 199 "
            pdb=" OG1 THR A 202 "
     model   vdw
     2.256 3.040
  ... (remaining 60679 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             0.370
  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:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     21.900
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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   0.074   8505  Z= 0.226
  Angle     :  0.738  16.502  11515  Z= 0.360
  Chirality :  0.041   0.203   1226
  Planarity :  0.005   0.090   1508
  Dihedral  : 21.029 123.539   3297
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 28.88 %
    Favored  : 71.00 %
  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:  1.22 (0.27), residues: 1000
  helix:  2.07 (0.21), residues: 605
  sheet: -0.25 (0.86), residues: 38
  loop : -1.35 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 345 
 HIS   0.003   0.001   HIS B 351 
 PHE   0.018   0.001   PHE A 110 
 TYR   0.019   0.001   TYR B 338 
 ARG   0.006   0.001   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 1.014 
Fit side-chains
REVERT: A  471 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7828 (mtt90)
REVERT: A  696 MET cc_start: 0.8437 (ttm) cc_final: 0.8191 (ttm)
REVERT: B  308 LEU cc_start: 0.8808 (tp) cc_final: 0.8494 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 108
  average time/residue: 0.1646
  time to fit residues: 26.6645
Evaluate side-chains
  102 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0170
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.3624

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN
B 276 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.144649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.100446 restraints weight = 15872.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.104462 restraints weight = 9655.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.107018 restraints weight = 7233.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.0804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8505  Z= 0.219
  Angle     :  0.644   9.885  11515  Z= 0.317
  Chirality :  0.041   0.198   1226
  Planarity :  0.005   0.062   1508
  Dihedral  : 14.835 110.359   1301
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 26.01 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.27), residues: 1000
  helix:  2.25 (0.21), residues: 614
  sheet:  0.11 (0.84), residues: 38
  loop : -1.28 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 345 
 HIS   0.005   0.001   HIS A 481 
 PHE   0.015   0.001   PHE A 622 
 TYR   0.020   0.001   TYR B 338 
 ARG   0.003   0.000   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A  234 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8151 (mp0)
REVERT: A  444 ARG cc_start: 0.8920 (ttm170) cc_final: 0.8373 (mtt-85)
REVERT: B  308 LEU cc_start: 0.8805 (tp) cc_final: 0.8504 (tp)
  outliers start: 22
  outliers final: 10
  residues processed: 122
  average time/residue: 0.1565
  time to fit residues: 28.9128
Evaluate side-chains
  110 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  674 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 481 HIS
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.145683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.102064 restraints weight = 16034.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.106346 restraints weight = 9356.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.109071 restraints weight = 6841.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8505  Z= 0.155
  Angle     :  0.595   9.555  11515  Z= 0.287
  Chirality :  0.040   0.245   1226
  Planarity :  0.004   0.057   1508
  Dihedral  : 13.004 107.517   1301
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 25.55 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.27), residues: 1000
  helix:  2.27 (0.21), residues: 623
  sheet:  0.56 (0.73), residues: 48
  loop : -1.15 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 345 
 HIS   0.005   0.001   HIS A 205 
 PHE   0.010   0.001   PHE A 331 
 TYR   0.017   0.001   TYR A 312 
 ARG   0.004   0.000   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7965 (pt0)
REVERT: A  185 TYR cc_start: 0.9338 (t80) cc_final: 0.8951 (t80)
REVERT: A  234 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8031 (mp0)
REVERT: A  444 ARG cc_start: 0.9002 (ttm170) cc_final: 0.8568 (mtt-85)
  outliers start: 28
  outliers final: 10
  residues processed: 129
  average time/residue: 0.1554
  time to fit residues: 30.2483
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  244 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 619 ASN ** 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 = 0.3934 r_free = 0.3934 target = 0.145765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.102013 restraints weight = 15643.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.106259 restraints weight = 9266.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.108816 restraints weight = 6825.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8505  Z= 0.165
  Angle     :  0.591   9.139  11515  Z= 0.284
  Chirality :  0.040   0.272   1226
  Planarity :  0.004   0.057   1508
  Dihedral  : 12.268 107.129   1301
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 26.12 %
    Favored  : 70.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.78 (0.27), residues: 1000
  helix:  2.33 (0.21), residues: 624
  sheet:  0.79 (0.75), residues: 48
  loop : -1.10 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.010   0.001   PHE A 676 
 TYR   0.026   0.001   TYR B 321 
 ARG   0.004   0.000   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7949 (pt0)
REVERT: A  185 TYR cc_start: 0.9365 (t80) cc_final: 0.8989 (t80)
REVERT: A  234 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8006 (mp0)
REVERT: A  444 ARG cc_start: 0.9003 (ttm170) cc_final: 0.8547 (mtt-85)
REVERT: B  345 TRP cc_start: 0.8667 (m-90) cc_final: 0.8424 (m-90)
  outliers start: 27
  outliers final: 14
  residues processed: 123
  average time/residue: 0.1647
  time to fit residues: 30.2398
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  347 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0980
   chunk 7 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN
A 481 HIS
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.147575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.104809 restraints weight = 15619.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.108496 restraints weight = 10059.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.110924 restraints weight = 7716.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8505  Z= 0.153
  Angle     :  0.601  11.186  11515  Z= 0.284
  Chirality :  0.040   0.278   1226
  Planarity :  0.004   0.055   1508
  Dihedral  : 11.663 107.035   1301
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 26.81 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.27), residues: 1000
  helix:  2.30 (0.21), residues: 628
  sheet:  0.94 (0.76), residues: 48
  loop : -1.02 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.010   0.001   PHE A 331 
 TYR   0.018   0.001   TYR B 337 
 ARG   0.005   0.000   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8287 (mm)
REVERT: A   86 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7933 (pt0)
REVERT: A  180 GLN cc_start: 0.9137 (tp40) cc_final: 0.8701 (tp-100)
REVERT: A  185 TYR cc_start: 0.9369 (t80) cc_final: 0.9011 (t80)
REVERT: A  234 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7941 (mp0)
REVERT: A  444 ARG cc_start: 0.9020 (ttm170) cc_final: 0.8519 (mtt-85)
REVERT: B  181 MET cc_start: 0.9443 (mmm) cc_final: 0.9018 (mmp)
REVERT: B  345 TRP cc_start: 0.8622 (m-90) cc_final: 0.8379 (m-90)
  outliers start: 28
  outliers final: 12
  residues processed: 123
  average time/residue: 0.1830
  time to fit residues: 33.3797
Evaluate side-chains
  112 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 1.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  347 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 619 ASN ** 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 = 0.3940 r_free = 0.3940 target = 0.146422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.103160 restraints weight = 15624.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.107206 restraints weight = 9331.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.109926 restraints weight = 6911.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8505  Z= 0.164
  Angle     :  0.615  11.339  11515  Z= 0.290
  Chirality :  0.040   0.290   1226
  Planarity :  0.004   0.055   1508
  Dihedral  : 11.229 107.092   1301
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 26.58 %
    Favored  : 69.85 %
  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:  1.87 (0.27), residues: 1000
  helix:  2.34 (0.21), residues: 626
  sheet:  1.01 (0.76), residues: 48
  loop : -0.98 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 345 
 HIS   0.004   0.001   HIS B 341 
 PHE   0.010   0.001   PHE A 676 
 TYR   0.016   0.001   TYR A 312 
 ARG   0.004   0.000   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8300 (mm)
REVERT: A   86 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7932 (pt0)
REVERT: A  185 TYR cc_start: 0.9395 (t80) cc_final: 0.9046 (t80)
REVERT: A  234 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7933 (mp0)
REVERT: A  444 ARG cc_start: 0.8977 (ttm170) cc_final: 0.8669 (mtt-85)
REVERT: B  113 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7458 (tt)
REVERT: B  181 MET cc_start: 0.9435 (mmm) cc_final: 0.9052 (mmp)
REVERT: B  345 TRP cc_start: 0.8700 (m-90) cc_final: 0.8438 (m-90)
  outliers start: 31
  outliers final: 17
  residues processed: 124
  average time/residue: 0.1611
  time to fit residues: 30.1419
Evaluate side-chains
  121 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0870
   chunk 56 optimal weight:    0.5980
   chunk 60 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
A 536 HIS
A 657 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.149745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.106853 restraints weight = 15691.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.111094 restraints weight = 9222.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.113941 restraints weight = 6755.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8505  Z= 0.158
  Angle     :  0.618  12.641  11515  Z= 0.290
  Chirality :  0.040   0.295   1226
  Planarity :  0.004   0.055   1508
  Dihedral  : 10.791 107.224   1301
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 27.04 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.27), residues: 1000
  helix:  2.37 (0.21), residues: 627
  sheet:  1.14 (0.77), residues: 48
  loop : -0.95 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP B 345 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.013   0.001   PHE B 256 
 TYR   0.013   0.001   TYR B 337 
 ARG   0.005   0.000   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8006 (pt0)
REVERT: A  185 TYR cc_start: 0.9398 (t80) cc_final: 0.9098 (t80)
REVERT: A  234 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7876 (mp0)
REVERT: A  444 ARG cc_start: 0.9012 (ttm170) cc_final: 0.8687 (mtt-85)
REVERT: B  113 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7557 (tt)
REVERT: B  181 MET cc_start: 0.9422 (mmm) cc_final: 0.9032 (mmp)
REVERT: B  345 TRP cc_start: 0.8662 (m-90) cc_final: 0.8436 (m-90)
  outliers start: 28
  outliers final: 19
  residues processed: 119
  average time/residue: 0.1496
  time to fit residues: 27.0453
Evaluate side-chains
  120 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 57 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0980
   chunk 62 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 95 optimal weight:    8.9990
   overall best weight:    1.4784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.144207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.100293 restraints weight = 15792.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.104258 restraints weight = 9604.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.106924 restraints weight = 7170.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8505  Z= 0.221
  Angle     :  0.644  13.477  11515  Z= 0.304
  Chirality :  0.041   0.319   1226
  Planarity :  0.004   0.057   1508
  Dihedral  : 10.421 106.266   1301
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 27.16 %
    Favored  : 69.28 %
  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:  1.95 (0.27), residues: 1000
  helix:  2.36 (0.21), residues: 627
  sheet:  1.21 (0.78), residues: 49
  loop : -0.92 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 345 
 HIS   0.005   0.001   HIS A 303 
 PHE   0.014   0.001   PHE A 676 
 TYR   0.013   0.001   TYR A 235 
 ARG   0.005   0.000   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7825 (pt0)
REVERT: A  180 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8743 (tp-100)
REVERT: A  185 TYR cc_start: 0.9399 (t80) cc_final: 0.9109 (t80)
REVERT: A  234 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7952 (mp0)
REVERT: A  444 ARG cc_start: 0.9038 (ttm170) cc_final: 0.8539 (mtt-85)
REVERT: B  113 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7620 (tt)
REVERT: B  181 MET cc_start: 0.9425 (mmm) cc_final: 0.9067 (mmp)
REVERT: B  244 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8526 (tt)
REVERT: B  345 TRP cc_start: 0.8713 (m-90) cc_final: 0.8464 (m-90)
  outliers start: 31
  outliers final: 22
  residues processed: 117
  average time/residue: 0.1578
  time to fit residues: 27.8332
Evaluate side-chains
  123 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 75 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 99 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 481 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.148056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.102821 restraints weight = 15650.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.107136 restraints weight = 9131.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.110018 restraints weight = 6682.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8505  Z= 0.184
  Angle     :  0.645  14.199  11515  Z= 0.300
  Chirality :  0.041   0.313   1226
  Planarity :  0.004   0.056   1508
  Dihedral  : 10.208 106.726   1301
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 27.96 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.27), residues: 1000
  helix:  2.40 (0.21), residues: 626
  sheet:  1.27 (0.78), residues: 49
  loop : -0.89 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 345 
 HIS   0.003   0.001   HIS A 205 
 PHE   0.012   0.001   PHE B 256 
 TYR   0.017   0.001   TYR B 338 
 ARG   0.006   0.000   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7831 (pt0)
REVERT: A  180 GLN cc_start: 0.9134 (tp-100) cc_final: 0.8752 (tp-100)
REVERT: A  185 TYR cc_start: 0.9390 (t80) cc_final: 0.9076 (t80)
REVERT: A  234 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7865 (mp0)
REVERT: A  444 ARG cc_start: 0.8968 (ttm170) cc_final: 0.8626 (mtt-85)
REVERT: B  113 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7522 (tt)
REVERT: B  345 TRP cc_start: 0.8697 (m-90) cc_final: 0.8486 (m-90)
  outliers start: 25
  outliers final: 21
  residues processed: 112
  average time/residue: 0.1559
  time to fit residues: 26.3322
Evaluate side-chains
  117 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0770
   chunk 60 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 80 optimal weight:    0.3980
   chunk 71 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.8942

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.145248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.102266 restraints weight = 16604.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.106469 restraints weight = 9881.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.109193 restraints weight = 7273.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8505  Z= 0.177
  Angle     :  0.648  14.552  11515  Z= 0.299
  Chirality :  0.041   0.318   1226
  Planarity :  0.004   0.056   1508
  Dihedral  :  9.957 107.067   1301
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 28.08 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.27), residues: 1000
  helix:  2.37 (0.21), residues: 628
  sheet:  1.35 (0.85), residues: 39
  loop : -0.98 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 345 
 HIS   0.003   0.001   HIS A 205 
 PHE   0.010   0.001   PHE A 676 
 TYR   0.016   0.001   TYR B 338 
 ARG   0.005   0.000   ARG A 471 

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7801 (pt0)
REVERT: A  180 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8740 (tp-100)
REVERT: A  185 TYR cc_start: 0.9397 (t80) cc_final: 0.9099 (t80)
REVERT: A  234 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7811 (mp0)
REVERT: A  444 ARG cc_start: 0.8972 (ttm170) cc_final: 0.8626 (mtt-85)
REVERT: B  113 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7657 (tt)
  outliers start: 27
  outliers final: 20
  residues processed: 118
  average time/residue: 0.1536
  time to fit residues: 27.3197
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 80 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.1182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.145364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.102046 restraints weight = 16792.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.106259 restraints weight = 9945.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.109023 restraints weight = 7308.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
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   0.036   8505  Z= 0.192
  Angle     :  0.644  14.197  11515  Z= 0.298
  Chirality :  0.041   0.329   1226
  Planarity :  0.004   0.057   1508
  Dihedral  :  9.758 107.486   1301
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 27.96 %
    Favored  : 69.28 %
  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:  1.97 (0.28), residues: 1000
  helix:  2.33 (0.21), residues: 633
  sheet:  1.37 (0.78), residues: 49
  loop : -0.88 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 345 
 HIS   0.003   0.001   HIS A 205 
 PHE   0.012   0.001   PHE B 256 
 TYR   0.014   0.001   TYR B 337 
 ARG   0.006   0.000   ARG A 471 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2566.60 seconds
wall clock time: 46 minutes 45.42 seconds (2805.42 seconds total)