Starting phenix.real_space_refine
on Thu Jun  5 01:18:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j3l_61118/06_2025/9j3l_61118.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j3l_61118/06_2025/9j3l_61118.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j3l_61118/06_2025/9j3l_61118.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j3l_61118/06_2025/9j3l_61118.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j3l_61118/06_2025/9j3l_61118.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j3l_61118/06_2025/9j3l_61118.cif"
  }
  resolution = 2.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.093
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      28      5.16       5
     C    3117      2.51       5
     N     742      2.21       5
     O     840      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4730
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3750
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 482, 3746
          Classifications: {'peptide': 482}
          Link IDs: {'PTRANS': 25, 'TRANS': 456}
      Conformer: "B"
        Number of residues, atoms: 482, 3746
          Classifications: {'peptide': 482}
          Link IDs: {'PTRANS': 25, 'TRANS': 456}
          bond proxies already assigned to first conformer: 3840
    Chain: "C"
      Number of atoms: 949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 949
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.89, per 1000 atoms: 1.03
  Number of scatterers: 4730
  At special positions: 0
  Unit cell: (71.61, 74.4, 110.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P       3     15.00
     O     840      8.00
     N     742      7.00
     C    3117      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " 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
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 969.4 milliseconds
  

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1112

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 4 sheets defined
      69.6% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 110 through 143
      removed outlier: 4.182A  pdb=" N   LYS A 115 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
      Proline residue:  A 118  - end of helix
      removed outlier: 3.668A  pdb=" N   ASP A 135 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASP A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 159
      removed outlier: 4.381A  pdb=" N   PHE A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   THR A 157 " --> pdb=" O   PRO A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 178
      removed outlier: 4.028A  pdb=" N   ASN A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   VAL A 177 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 187
    Processing helix  chain 'A' and resid 188 through 201
    Processing helix  chain 'A' and resid 203 through 207
      removed outlier: 4.505A  pdb=" N   ASN A 207 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 223
    Processing helix  chain 'A' and resid 226 through 235
      removed outlier: 3.715A  pdb=" N   ILE A 232 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   LEU A 233 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 252
      removed outlier: 3.690A  pdb=" N   GLY A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 263
      removed outlier: 3.606A  pdb=" N   GLN A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
    Processing helix  chain 'A' and resid 273 through 297
      removed outlier: 3.503A  pdb=" N   LEU A 285 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 335
      removed outlier: 4.046A  pdb=" N   ILE A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 365
    Processing helix  chain 'A' and resid 365 through 397
      removed outlier: 3.752A  pdb=" N   ASP A 370 " --> pdb=" O   PRO A 366 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU A 371 " --> pdb=" O   TYR A 367 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   GLY A 379 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ILE A 382 " --> pdb=" O   TYR A 378 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ASN A 383 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   THR A 388 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 433
      removed outlier: 4.459A  pdb=" N   GLN A 426 " --> pdb=" O   MET A 422 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   TYR A 427 " --> pdb=" O   LEU A 423 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   ASN A 430 " --> pdb=" O   GLN A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 457
      removed outlier: 3.632A  pdb=" N   LYS A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE A 440 " --> pdb=" O   VAL A 436 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   THR A 441 " --> pdb=" O   ALA A 437 " (cutoff:3.500A)
      Proline residue:  A 442  - end of helix
    Processing helix  chain 'A' and resid 464 through 469
    Processing helix  chain 'A' and resid 472 through 504
      removed outlier: 3.539A  pdb=" N   SER A 494 " --> pdb=" O   SER A 490 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   ASP A 497 " --> pdb=" O   TYR A 493 " (cutoff:3.500A)
      Proline residue:  A 498  - end of helix
      removed outlier: 3.610A  pdb=" N   TYR A 504 " --> pdb=" O   LYS A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 543
      removed outlier: 3.558A  pdb=" N   ALA A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASP A 520 " --> pdb=" O   LYS A 516 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   VAL A 521 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL A 522 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
      Proline residue:  A 525  - end of helix
      removed outlier: 3.843A  pdb=" N   ALA A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLN A 535 " --> pdb=" O   GLY A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 568
      removed outlier: 3.519A  pdb=" N   ALA A 567 " --> pdb=" O   TRP A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 581
      removed outlier: 3.867A  pdb=" N   GLU A 581 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
    Processing helix  chain 'C' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 105
    Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.031A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   SER C 119 " --> pdb=" O   GLY C  10 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL C  12 " --> pdb=" O   SER C 119 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.031A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   SER C 119 " --> pdb=" O   GLY C  10 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL C  12 " --> pdb=" O   SER C 119 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   VAL C 101 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   TYR C 105 " --> pdb=" O   VAL C 101 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    918 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: 1.28

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1398
        1.34 -     1.46: 1037
        1.46 -     1.58: 2369
        1.58 -     1.69: 5
        1.69 -     1.81: 48
  Bond restraints: 4857
  Sorted by residual:
  bond pdb=" C4  ATP A 701 "
       pdb=" N9  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.374  1.303  0.071 1.00e-02 1.00e+04 5.02e+01
  bond pdb=" C5  ATP A 701 "
       pdb=" N7  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.387  1.318  0.069 1.00e-02 1.00e+04 4.82e+01
  bond pdb=" C4  ATP A 701 "
       pdb=" C5  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.388  1.450 -0.062 1.00e-02 1.00e+04 3.84e+01
  bond pdb=" O5' ATP A 701 "
       pdb=" PA  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.579  1.633 -0.054 1.10e-02 8.26e+03 2.38e+01
  bond pdb=" C8  ATP A 701 "
       pdb=" N9  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.370  1.312  0.058 1.20e-02 6.94e+03 2.33e+01
  ... (remaining 4852 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.31: 6541
        3.31 -     6.62: 58
        6.62 -     9.93: 7
        9.93 -    13.25: 2
       13.25 -    16.56: 1
  Bond angle restraints: 6609
  Sorted by residual:
  angle pdb=" PB  ATP A 701 "
        pdb=" O3B ATP A 701 "
        pdb=" PG  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     139.87  123.31   16.56 1.00e+00 1.00e+00 2.74e+02
  angle pdb=" PA  ATP A 701 "
        pdb=" O3A ATP A 701 "
        pdb=" PB  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     136.83  127.81    9.02 1.00e+00 1.00e+00 8.13e+01
  angle pdb=" C5  ATP A 701 "
        pdb=" C4  ATP A 701 "
        pdb=" N3  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     126.80  118.78    8.02 1.00e+00 1.00e+00 6.43e+01
  angle pdb=" N3  ATP A 701 "
        pdb=" C4  ATP A 701 "
        pdb=" N9  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     127.04  134.83   -7.79 1.15e+00 7.59e-01 4.60e+01
  angle pdb=" N   TYR A 208 "
        pdb=" CA  TYR A 208 "
        pdb=" C   TYR A 208 "
      ideal   model   delta    sigma   weight residual
     114.56  106.39    8.17 1.27e+00 6.20e-01 4.14e+01
  ... (remaining 6604 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 2624
       17.42 -    34.84: 184
       34.84 -    52.26: 42
       52.26 -    69.68: 10
       69.68 -    87.10: 1
  Dihedral angle restraints: 2861
    sinusoidal: 1114
      harmonic: 1747
  Sorted by residual:
  dihedral pdb=" CA  GLU A 349 "
           pdb=" C   GLU A 349 "
           pdb=" N   LYS A 350 "
           pdb=" CA  LYS A 350 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.40  -27.60     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  GLN A 426 "
           pdb=" C   GLN A 426 "
           pdb=" N   TYR A 427 "
           pdb=" CA  TYR A 427 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.56   26.44     0      5.00e+00 4.00e-02 2.80e+01
  dihedral pdb=" CA  LYS A 352 "
           pdb=" C   LYS A 352 "
           pdb=" N   MET A 353 "
           pdb=" CA  MET A 353 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.96  -24.04     0      5.00e+00 4.00e-02 2.31e+01
  ... (remaining 2858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 442
       0.029 -    0.058: 194
       0.058 -    0.088: 83
       0.088 -    0.117: 23
       0.117 -    0.146: 9
  Chirality restraints: 751
  Sorted by residual:
  chirality pdb=" CA  TYR A 208 "
            pdb=" N   TYR A 208 "
            pdb=" C   TYR A 208 "
            pdb=" CB  TYR A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.32e-01
  chirality pdb=" CG  LEU A 446 "
            pdb=" CB  LEU A 446 "
            pdb=" CD1 LEU A 446 "
            pdb=" CD2 LEU A 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  ASN A 160 "
            pdb=" N   ASN A 160 "
            pdb=" C   ASN A 160 "
            pdb=" CB  ASN A 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 748 not shown)

  Planarity restraints: 803
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 492 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.39e+00
        pdb=" C   LYS A 492 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   LYS A 492 "    0.015 2.00e-02 2.50e+03
        pdb=" N   TYR A 493 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 203 "    0.038 5.00e-02 4.00e+02   5.66e-02 5.12e+00
        pdb=" N   PRO A 204 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA APRO A 204 "    0.028 5.00e-02 4.00e+02
        pdb=" CD APRO A 204 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 203 "    0.037 5.00e-02 4.00e+02   5.58e-02 4.99e+00
        pdb=" N   PRO A 204 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA BPRO A 204 "    0.028 5.00e-02 4.00e+02
        pdb=" CD BPRO A 204 "    0.031 5.00e-02 4.00e+02
  ... (remaining 800 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 889
        2.77 -     3.30: 4719
        3.30 -     3.83: 8299
        3.83 -     4.37: 10174
        4.37 -     4.90: 16780
  Nonbonded interactions: 40861
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A 210 "
            pdb=" OG  SER A 237 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   THR A 388 "
            pdb=" OG  SER A 391 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   MET A 168 "
            pdb=" OG1 THR A 172 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ALA A 567 "
            pdb=" N   GLU A 571 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" O   LYS A 314 "
            pdb=" OG  SER A 318 "
     model   vdw
     2.280 3.040
  ... (remaining 40856 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.370
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:11.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
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   0.071   4858  Z= 0.268
  Angle     :  0.787  16.558   6611  Z= 0.480
  Chirality :  0.041   0.146    751
  Planarity :  0.006   0.057    803
  Dihedral  : 13.033  87.096   1746
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  0.00 %
    Favored  : 99.60 %
  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: -1.92 (0.33), residues: 599
  helix: -1.10 (0.24), residues: 402
  sheet: -1.46 (0.75), residues: 42
  loop : -1.08 (0.53), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 333 
 HIS   0.001   0.001   HIS A 210 
 PHE   0.016   0.001   PHE A 452 
 TYR   0.027   0.002   TYR A 337 
 ARG   0.010   0.001   ARG A 336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20363 (  316)
  hydrogen bonds       : angle       8.63110 (  918)
  SS BOND              : bond        0.00110 (    1)
  SS BOND              : angle       0.87709 (    2)
  covalent geometry    : bond        0.00386 ( 4857)
  covalent geometry    : angle       0.78729 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  167 PHE cc_start: 0.8247 (t80) cc_final: 0.7990 (t80)
REVERT: A  170 LEU cc_start: 0.8960 (tp) cc_final: 0.8754 (tp)
REVERT: A  173 LYS cc_start: 0.8125 (tmtt) cc_final: 0.7561 (tptm)
REVERT: A  294 TYR cc_start: 0.8984 (t80) cc_final: 0.8535 (t80)
REVERT: A  329 LEU cc_start: 0.8496 (tp) cc_final: 0.8177 (mt)
REVERT: A  353 MET cc_start: 0.6887 (tpt) cc_final: 0.6645 (tpt)
REVERT: A  356 MET cc_start: 0.3912 (mmt) cc_final: 0.3627 (mmt)
REVERT: C   43 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8156 (mtpt)
REVERT: C   77 THR cc_start: 0.8639 (m) cc_final: 0.8431 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 1.0349
  time to fit residues: 117.6501
Evaluate side-chains
  93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0980
   chunk 28 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
C  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.138190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.102279 restraints weight = 8670.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.09
r_work: 0.2996 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4858  Z= 0.173
  Angle     :  0.665   9.360   6611  Z= 0.348
  Chirality :  0.043   0.169    751
  Planarity :  0.005   0.043    803
  Dihedral  :  7.803  63.957    684
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  8.70 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.34), residues: 599
  helix: -0.32 (0.25), residues: 407
  sheet: -1.52 (0.63), residues: 48
  loop : -0.46 (0.55), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 563 
 HIS   0.002   0.001   HIS A 210 
 PHE   0.022   0.002   PHE A 257 
 TYR   0.014   0.002   TYR A 378 
 ARG   0.004   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05142 (  316)
  hydrogen bonds       : angle       5.90695 (  918)
  SS BOND              : bond        0.00250 (    1)
  SS BOND              : angle       1.62275 (    2)
  covalent geometry    : bond        0.00375 ( 4857)
  covalent geometry    : angle       0.66438 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.536 
Fit side-chains
REVERT: A  158 TRP cc_start: 0.8715 (m100) cc_final: 0.8289 (m100)
REVERT: A  169 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8599 (mt)
REVERT: A  173 LYS cc_start: 0.8100 (tmtt) cc_final: 0.7546 (tptm)
REVERT: A  294 TYR cc_start: 0.9048 (t80) cc_final: 0.8517 (t80)
REVERT: A  353 MET cc_start: 0.6856 (tpt) cc_final: 0.6632 (tpt)
REVERT: A  356 MET cc_start: 0.3783 (mmt) cc_final: 0.3539 (mmt)
REVERT: A  554 MET cc_start: 0.8315 (mtm) cc_final: 0.8013 (mtp)
REVERT: C   46 GLU cc_start: 0.8567 (tt0) cc_final: 0.8309 (tt0)
  outliers start: 6
  outliers final: 0
  residues processed: 100
  average time/residue: 0.8297
  time to fit residues: 87.6333
Evaluate side-chains
  92 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 12 optimal weight:    0.0070
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0040
   chunk 51 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.3410

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN
A 401 ASN
C  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.140559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.104111 restraints weight = 11621.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.35
r_work: 0.3008 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4858  Z= 0.132
  Angle     :  0.604   7.824   6611  Z= 0.312
  Chirality :  0.040   0.148    751
  Planarity :  0.005   0.038    803
  Dihedral  :  7.041  56.939    684
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 11.86 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.35), residues: 599
  helix:  0.41 (0.26), residues: 404
  sheet: -1.55 (0.56), residues: 48
  loop : -0.21 (0.55), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 309 
 HIS   0.001   0.000   HIS A 210 
 PHE   0.020   0.002   PHE A 257 
 TYR   0.012   0.001   TYR A 378 
 ARG   0.003   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04281 (  316)
  hydrogen bonds       : angle       5.29648 (  918)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       1.17344 (    2)
  covalent geometry    : bond        0.00283 ( 4857)
  covalent geometry    : angle       0.60378 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.593 
Fit side-chains
REVERT: A  169 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8570 (mt)
REVERT: A  173 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7493 (tptm)
REVERT: A  294 TYR cc_start: 0.9067 (t80) cc_final: 0.8488 (t80)
REVERT: A  353 MET cc_start: 0.6949 (tpt) cc_final: 0.6620 (tpt)
REVERT: A  356 MET cc_start: 0.3631 (mmt) cc_final: 0.3354 (mmt)
  outliers start: 4
  outliers final: 0
  residues processed: 102
  average time/residue: 0.8930
  time to fit residues: 95.9964
Evaluate side-chains
  94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0980
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.138894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.103344 restraints weight = 10680.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.24
r_work: 0.3015 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   4858  Z= 0.153
  Angle     :  0.603   7.236   6611  Z= 0.311
  Chirality :  0.041   0.157    751
  Planarity :  0.004   0.037    803
  Dihedral  :  6.780  61.831    684
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 14.03 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.35), residues: 599
  helix:  0.60 (0.26), residues: 404
  sheet: -1.30 (0.59), residues: 46
  loop : -0.01 (0.56), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 309 
 HIS   0.001   0.001   HIS A 210 
 PHE   0.018   0.002   PHE A 257 
 TYR   0.013   0.001   TYR A 378 
 ARG   0.004   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04295 (  316)
  hydrogen bonds       : angle       5.16259 (  918)
  SS BOND              : bond        0.00127 (    1)
  SS BOND              : angle       1.33952 (    2)
  covalent geometry    : bond        0.00347 ( 4857)
  covalent geometry    : angle       0.60284 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A  169 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8542 (mt)
REVERT: A  173 LYS cc_start: 0.8024 (tmtt) cc_final: 0.7474 (tptm)
REVERT: A  294 TYR cc_start: 0.9073 (t80) cc_final: 0.8548 (t80)
REVERT: A  353 MET cc_start: 0.6876 (tpt) cc_final: 0.6599 (tpt)
REVERT: A  356 MET cc_start: 0.3862 (mmt) cc_final: 0.3617 (mmt)
REVERT: A  554 MET cc_start: 0.8168 (mtp) cc_final: 0.7877 (mtp)
  outliers start: 6
  outliers final: 1
  residues processed: 93
  average time/residue: 0.8897
  time to fit residues: 87.1222
Evaluate side-chains
  90 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  312 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 13 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.138494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.101970 restraints weight = 9984.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.21
r_work: 0.2989 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4858  Z= 0.152
  Angle     :  0.591   6.753   6611  Z= 0.307
  Chirality :  0.041   0.166    751
  Planarity :  0.004   0.036    803
  Dihedral  :  6.686  62.692    684
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.24 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.35), residues: 599
  helix:  0.65 (0.26), residues: 404
  sheet: -1.23 (0.59), residues: 46
  loop :  0.09 (0.56), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 309 
 HIS   0.002   0.001   HIS A 210 
 PHE   0.017   0.002   PHE A 257 
 TYR   0.013   0.001   TYR A 378 
 ARG   0.002   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04201 (  316)
  hydrogen bonds       : angle       5.07603 (  918)
  SS BOND              : bond        0.00103 (    1)
  SS BOND              : angle       1.23962 (    2)
  covalent geometry    : bond        0.00340 ( 4857)
  covalent geometry    : angle       0.59064 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  169 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8538 (mt)
REVERT: A  173 LYS cc_start: 0.7981 (tmtt) cc_final: 0.7425 (tptm)
REVERT: A  294 TYR cc_start: 0.9076 (t80) cc_final: 0.8536 (t80)
REVERT: A  336 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7859 (ttt-90)
REVERT: A  353 MET cc_start: 0.6927 (tpt) cc_final: 0.6616 (tpt)
REVERT: A  356 MET cc_start: 0.3821 (mmt) cc_final: 0.3501 (mmt)
REVERT: A  512 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6149 (ttmt)
  outliers start: 9
  outliers final: 5
  residues processed: 93
  average time/residue: 0.8518
  time to fit residues: 83.4945
Evaluate side-chains
  93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   84 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 536 GLN
C  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.136079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.098675 restraints weight = 12943.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.45
r_work: 0.2844 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4858  Z= 0.193
  Angle     :  0.615   7.082   6611  Z= 0.320
  Chirality :  0.043   0.163    751
  Planarity :  0.004   0.036    803
  Dihedral  :  6.771  65.392    684
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.83 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.35), residues: 599
  helix:  0.57 (0.26), residues: 407
  sheet: -1.23 (0.60), residues: 46
  loop :  0.03 (0.56), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 563 
 HIS   0.002   0.001   HIS A 210 
 PHE   0.018   0.002   PHE A 257 
 TYR   0.015   0.002   TYR A 378 
 ARG   0.003   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04428 (  316)
  hydrogen bonds       : angle       5.18000 (  918)
  SS BOND              : bond        0.00113 (    1)
  SS BOND              : angle       1.47636 (    2)
  covalent geometry    : bond        0.00445 ( 4857)
  covalent geometry    : angle       0.61504 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A  169 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8525 (mt)
REVERT: A  173 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7423 (tptm)
REVERT: A  294 TYR cc_start: 0.9029 (t80) cc_final: 0.8523 (t80)
REVERT: A  353 MET cc_start: 0.6841 (tpt) cc_final: 0.6587 (tpt)
REVERT: A  356 MET cc_start: 0.3896 (mmt) cc_final: 0.3595 (mmt)
REVERT: A  512 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6163 (ttmt)
  outliers start: 9
  outliers final: 3
  residues processed: 93
  average time/residue: 0.8757
  time to fit residues: 85.9533
Evaluate side-chains
  92 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain C residue   84 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0040
   chunk 26 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
C  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.138177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.101813 restraints weight = 10745.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.26
r_work: 0.2965 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4858  Z= 0.143
  Angle     :  0.579   6.809   6611  Z= 0.301
  Chirality :  0.041   0.155    751
  Planarity :  0.004   0.036    803
  Dihedral  :  6.581  64.145    684
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.83 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.35), residues: 599
  helix:  0.73 (0.26), residues: 405
  sheet: -1.19 (0.61), residues: 46
  loop :  0.15 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 309 
 HIS   0.001   0.001   HIS A 210 
 PHE   0.018   0.002   PHE A 257 
 TYR   0.013   0.001   TYR A 378 
 ARG   0.002   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  316)
  hydrogen bonds       : angle       5.02484 (  918)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       1.12226 (    2)
  covalent geometry    : bond        0.00318 ( 4857)
  covalent geometry    : angle       0.57865 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.498 
Fit side-chains
REVERT: A  169 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8553 (mt)
REVERT: A  173 LYS cc_start: 0.8071 (tmtt) cc_final: 0.7445 (tptm)
REVERT: A  294 TYR cc_start: 0.9074 (t80) cc_final: 0.8533 (t80)
REVERT: A  336 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7929 (ttt-90)
REVERT: A  353 MET cc_start: 0.6906 (tpt) cc_final: 0.6560 (tpt)
REVERT: A  356 MET cc_start: 0.4078 (mmt) cc_final: 0.3704 (mmt)
REVERT: A  512 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6056 (ttmt)
  outliers start: 10
  outliers final: 4
  residues processed: 90
  average time/residue: 0.9292
  time to fit residues: 88.3673
Evaluate side-chains
  91 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain C residue   84 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0870
   chunk 33 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 5 optimal weight:    0.4980
   chunk 12 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
C  39 GLN
C  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.138771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.103600 restraints weight = 7771.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.96
r_work: 0.3018 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4858  Z= 0.135
  Angle     :  0.578   7.191   6611  Z= 0.300
  Chirality :  0.040   0.152    751
  Planarity :  0.004   0.035    803
  Dihedral  :  6.480  63.660    684
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.43 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.35), residues: 599
  helix:  0.87 (0.26), residues: 402
  sheet: -1.13 (0.61), residues: 46
  loop : -0.11 (0.55), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 258 
 HIS   0.001   0.001   HIS A 210 
 PHE   0.017   0.002   PHE A 257 
 TYR   0.013   0.001   TYR A 378 
 ARG   0.003   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04027 (  316)
  hydrogen bonds       : angle       4.98489 (  918)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       1.13020 (    2)
  covalent geometry    : bond        0.00300 ( 4857)
  covalent geometry    : angle       0.57778 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A  169 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8538 (mt)
REVERT: A  173 LYS cc_start: 0.8010 (tmtt) cc_final: 0.7381 (tptm)
REVERT: A  294 TYR cc_start: 0.9014 (t80) cc_final: 0.8419 (t80)
REVERT: A  353 MET cc_start: 0.6887 (tpt) cc_final: 0.6553 (tpt)
REVERT: A  356 MET cc_start: 0.4132 (mmt) cc_final: 0.3766 (mmt)
REVERT: A  512 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.5943 (ttmt)
  outliers start: 7
  outliers final: 4
  residues processed: 90
  average time/residue: 0.9025
  time to fit residues: 85.6546
Evaluate side-chains
  91 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain C residue   84 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 5 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.138941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.101955 restraints weight = 10550.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.28
r_work: 0.2974 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4858  Z= 0.148
  Angle     :  0.583   6.769   6611  Z= 0.303
  Chirality :  0.041   0.155    751
  Planarity :  0.004   0.036    803
  Dihedral  :  6.505  63.852    684
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.62 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.35), residues: 599
  helix:  0.93 (0.26), residues: 400
  sheet: -1.10 (0.62), residues: 46
  loop : -0.20 (0.54), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 258 
 HIS   0.001   0.001   HIS A 210 
 PHE   0.017   0.002   PHE A 257 
 TYR   0.013   0.001   TYR A 378 
 ARG   0.002   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04114 (  316)
  hydrogen bonds       : angle       5.00510 (  918)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       1.21742 (    2)
  covalent geometry    : bond        0.00335 ( 4857)
  covalent geometry    : angle       0.58231 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.550 
Fit side-chains
REVERT: A  169 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8553 (mt)
REVERT: A  173 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7415 (tptm)
REVERT: A  294 TYR cc_start: 0.9075 (t80) cc_final: 0.8473 (t80)
REVERT: A  353 MET cc_start: 0.6958 (tpt) cc_final: 0.6589 (tpt)
REVERT: A  356 MET cc_start: 0.4119 (mmt) cc_final: 0.3768 (mmt)
REVERT: A  512 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.5840 (ttmt)
  outliers start: 8
  outliers final: 5
  residues processed: 91
  average time/residue: 1.0090
  time to fit residues: 97.0286
Evaluate side-chains
  93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain C residue   84 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:    0.0770
   chunk 17 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0980
   chunk 39 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.138664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.102097 restraints weight = 11494.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.34
r_work: 0.2976 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4858  Z= 0.138
  Angle     :  0.582   7.036   6611  Z= 0.303
  Chirality :  0.041   0.152    751
  Planarity :  0.004   0.036    803
  Dihedral  :  6.430  63.358    684
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.82 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.35), residues: 599
  helix:  0.97 (0.26), residues: 402
  sheet: -1.08 (0.62), residues: 46
  loop : -0.09 (0.55), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 258 
 HIS   0.001   0.001   HIS A 210 
 PHE   0.016   0.002   PHE A 257 
 TYR   0.012   0.001   TYR A 378 
 ARG   0.002   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04036 (  316)
  hydrogen bonds       : angle       4.97624 (  918)
  SS BOND              : bond        0.00063 (    1)
  SS BOND              : angle       1.13488 (    2)
  covalent geometry    : bond        0.00308 ( 4857)
  covalent geometry    : angle       0.58163 ( 6609)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  169 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8557 (mt)
REVERT: A  173 LYS cc_start: 0.7984 (tmtt) cc_final: 0.7420 (tptm)
REVERT: A  294 TYR cc_start: 0.9057 (t80) cc_final: 0.8475 (t80)
REVERT: A  353 MET cc_start: 0.6934 (tpt) cc_final: 0.6570 (tpt)
REVERT: A  356 MET cc_start: 0.4175 (mmt) cc_final: 0.3824 (mmt)
REVERT: A  512 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.5860 (ttmt)
  outliers start: 8
  outliers final: 5
  residues processed: 91
  average time/residue: 1.4358
  time to fit residues: 138.9552
Evaluate side-chains
  94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 1.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain C residue   84 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 52 optimal weight:    0.0270
   chunk 45 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0970
   chunk 14 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.139898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.102155 restraints weight = 13576.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.54
r_work: 0.2969 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4858  Z= 0.136
  Angle     :  0.576   6.696   6611  Z= 0.300
  Chirality :  0.041   0.152    751
  Planarity :  0.004   0.036    803
  Dihedral  :  6.375  63.279    684
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.22 %
    Favored  : 83.00 %
  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:  0.74 (0.35), residues: 599
  helix:  0.99 (0.26), residues: 402
  sheet: -1.06 (0.63), residues: 46
  loop : -0.07 (0.54), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 309 
 HIS   0.001   0.000   HIS A 210 
 PHE   0.016   0.002   PHE A 257 
 TYR   0.013   0.001   TYR A 378 
 ARG   0.002   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  316)
  hydrogen bonds       : angle       4.96383 (  918)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       1.12637 (    2)
  covalent geometry    : bond        0.00304 ( 4857)
  covalent geometry    : angle       0.57543 ( 6609)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4663.21 seconds
wall clock time: 83 minutes 52.92 seconds (5032.92 seconds total)