Starting phenix.real_space_refine
on Tue Mar 11 19:43:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j4x_61138/03_2025/9j4x_61138.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j4x_61138/03_2025/9j4x_61138.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j4x_61138/03_2025/9j4x_61138.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j4x_61138/03_2025/9j4x_61138.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j4x_61138/03_2025/9j4x_61138.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j4x_61138/03_2025/9j4x_61138.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.103
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       4      5.49       5
     S      30      5.16       5
     C    4462      2.51       5
     N    1024      2.21       5
     O    1068      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3186
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 14, 'TRANS': 367}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3186
          Classifications: {'peptide': 382}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 367}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 108
          Unusual residues: {'PC1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 108
          Unusual residues: {'PC1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.25, per 1000 atoms: 0.80
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (125.19, 66.34, 75.97, 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      30     16.00
     P       4     15.00
     O    1068      8.00
     N    1024      7.00
     C    4462      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.04
  Conformation dependent library (CDL) restraints added in 849.1 milliseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 0 sheets defined
      79.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 258
    Processing helix  chain 'A' and resid 267 through 296
      removed outlier: 3.686A  pdb=" N   ILE A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   ARG A 273 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 312 through 336
    Processing helix  chain 'A' and resid 337 through 340
      removed outlier: 3.530A  pdb=" N   SER A 340 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 337 through 340'
    Processing helix  chain 'A' and resid 345 through 360
      removed outlier: 3.979A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.571A  pdb=" N   ASN A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 3.723A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 453
      removed outlier: 3.575A  pdb=" N   CYS A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 471
    Processing helix  chain 'A' and resid 472 through 503
      removed outlier: 3.934A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ASN A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA A 480 " --> pdb=" O   HIS A 476 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG A 502 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 4.334A  pdb=" N   LEU A 513 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TRP A 528 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 582
      removed outlier: 4.081A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 618
      Proline residue:  A 598  - end of helix
      removed outlier: 3.750A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 623
      removed outlier: 3.605A  pdb=" N   GLU A 622 " --> pdb=" O   ASN A 619 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   PHE A 623 " --> pdb=" O   CYS A 620 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 619 through 623'
    Processing helix  chain 'B' and resid 230 through 257
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.782A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 312 through 336
    Processing helix  chain 'B' and resid 345 through 360
      removed outlier: 4.081A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 384 through 387
    Processing helix  chain 'B' and resid 390 through 417
      removed outlier: 5.940A  pdb=" N   VAL B 405 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 453
    Processing helix  chain 'B' and resid 453 through 471
    Processing helix  chain 'B' and resid 472 through 499
      removed outlier: 4.285A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   VAL B 478 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.588A  pdb=" N   PHE B 510 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 581
      removed outlier: 3.522A  pdb=" N   TYR B 560 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER B 581 " --> pdb=" O   ILE B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 619
      Proline residue:  B 598  - end of helix
      removed outlier: 3.760A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 623
      removed outlier: 4.414A  pdb=" N   PHE B 623 " --> pdb=" O   CYS B 620 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 620 through 623'

    438 hydrogen bonds defined for protein.
    1311 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: 1.69

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 989
        1.32 -     1.44: 2066
        1.44 -     1.57: 3691
        1.57 -     1.69: 8
        1.69 -     1.81: 42
  Bond restraints: 6796
  Sorted by residual:
  bond pdb=" CG  GLN A 399 "
       pdb=" CD  GLN A 399 "
    ideal  model  delta    sigma   weight residual
    1.516  1.492  0.024 2.50e-02 1.60e+03 9.11e-01
  bond pdb=" C   ALA A 337 "
       pdb=" N   PRO A 338 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 8.26e-01
  bond pdb=" N   GLY A 589 "
       pdb=" CA  GLY A 589 "
    ideal  model  delta    sigma   weight residual
    1.449  1.461 -0.012 1.45e-02 4.76e+03 6.89e-01
  bond pdb=" C   VAL B 567 "
       pdb=" O   VAL B 567 "
    ideal  model  delta    sigma   weight residual
    1.237  1.246 -0.009 1.13e-02 7.83e+03 6.38e-01
  bond pdb=" CB  CYS B 463 "
       pdb=" SG  CYS B 463 "
    ideal  model  delta    sigma   weight residual
    1.808  1.783  0.025 3.30e-02 9.18e+02 5.56e-01
  ... (remaining 6791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 8820
        1.11 -     2.21: 315
        2.21 -     3.32: 39
        3.32 -     4.43: 14
        4.43 -     5.53: 14
  Bond angle restraints: 9202
  Sorted by residual:
  angle pdb=" N   GLU A 260 "
        pdb=" CA  GLU A 260 "
        pdb=" C   GLU A 260 "
      ideal   model   delta    sigma   weight residual
     114.62  109.21    5.41 1.14e+00 7.69e-01 2.26e+01
  angle pdb=" CA  GLU A 260 "
        pdb=" C   GLU A 260 "
        pdb=" N   THR A 261 "
      ideal   model   delta    sigma   weight residual
     119.71  115.09    4.62 1.17e+00 7.31e-01 1.56e+01
  angle pdb=" N   ARG A 270 "
        pdb=" CA  ARG A 270 "
        pdb=" C   ARG A 270 "
      ideal   model   delta    sigma   weight residual
     114.75  110.75    4.00 1.26e+00 6.30e-01 1.01e+01
  angle pdb=" C   ILE A 269 "
        pdb=" N   ARG A 270 "
        pdb=" CA  ARG A 270 "
      ideal   model   delta    sigma   weight residual
     121.52  126.81   -5.29 1.74e+00 3.30e-01 9.23e+00
  angle pdb=" N   VAL A 509 "
        pdb=" CA  VAL A 509 "
        pdb=" C   VAL A 509 "
      ideal   model   delta    sigma   weight residual
     113.00  109.06    3.94 1.30e+00 5.92e-01 9.17e+00
  ... (remaining 9197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.54: 3592
       16.54 -    33.08: 236
       33.08 -    49.61: 62
       49.61 -    66.15: 25
       66.15 -    82.69: 3
  Dihedral angle restraints: 3918
    sinusoidal: 1668
      harmonic: 2250
  Sorted by residual:
  dihedral pdb=" CA  ILE A 269 "
           pdb=" C   ILE A 269 "
           pdb=" N   ARG A 270 "
           pdb=" CA  ARG A 270 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.18   31.82     0      5.00e+00 4.00e-02 4.05e+01
  dihedral pdb=" CA  PHE A 257 "
           pdb=" C   PHE A 257 "
           pdb=" N   LYS A 258 "
           pdb=" CA  LYS A 258 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.24  -18.76     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  THR A 383 "
           pdb=" C   THR A 383 "
           pdb=" N   ALA A 384 "
           pdb=" CA  ALA A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.29  -17.71     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 3915 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 659
       0.035 -    0.069: 239
       0.069 -    0.103: 73
       0.103 -    0.138: 13
       0.138 -    0.172: 2
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" CB  ILE A 269 "
            pdb=" CA  ILE A 269 "
            pdb=" CG1 ILE A 269 "
            pdb=" CG2 ILE A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.42e-01
  chirality pdb=" CA  TRP A 266 "
            pdb=" N   TRP A 266 "
            pdb=" C   TRP A 266 "
            pdb=" CB  TRP A 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.42e-01
  chirality pdb=" CA  ILE A 342 "
            pdb=" N   ILE A 342 "
            pdb=" C   ILE A 342 "
            pdb=" CB  ILE A 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 983 not shown)

  Planarity restraints: 1098
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 563 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   ILE A 563 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ILE A 563 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE A 564 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 566 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.81e+00
        pdb=" C   ASP A 566 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ASP A 566 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL A 567 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 306 "    0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO A 307 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 307 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 307 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1095 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 101
        2.69 -     3.24: 6660
        3.24 -     3.80: 11036
        3.80 -     4.35: 14289
        4.35 -     4.90: 24201
  Nonbonded interactions: 56287
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 271 "
            pdb=" OH  TYR A 352 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" O   LYS B 482 "
            pdb=" OG1 THR B 485 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OE1 GLU B 318 "
            pdb=" OH  TYR B 367 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" NH2 ARG A 466 "
            pdb=" O   GLY A 621 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   ILE B 271 "
            pdb=" OH  TYR B 352 "
     model   vdw
     2.247 3.040
  ... (remaining 56282 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 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:             0.990
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.140
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
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      :  0.003   0.028   6796  Z= 0.205
  Angle     :  0.517   5.533   9202  Z= 0.294
  Chirality :  0.039   0.172    986
  Planarity :  0.004   0.033   1098
  Dihedral  : 12.984  82.689   2466
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  6.05 %
    Favored  : 92.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.84 (0.30), residues: 756
  helix:  1.42 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -2.42 (0.42), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 395 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.015   0.001   PHE B 610 
 TYR   0.012   0.001   TYR A 553 
 ARG   0.002   0.000   ARG B 611 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A  318 GLU cc_start: 0.8815 (tt0) cc_final: 0.8511 (tt0)
REVERT: A  376 LYS cc_start: 0.7836 (mttt) cc_final: 0.7308 (mmtm)
REVERT: A  394 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8093 (t80)
REVERT: A  471 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7800 (mmtm)
REVERT: A  506 ASP cc_start: 0.7111 (m-30) cc_final: 0.6883 (p0)
REVERT: A  523 CYS cc_start: 0.8530 (t) cc_final: 0.8153 (m)
REVERT: A  538 ASP cc_start: 0.8084 (t70) cc_final: 0.7499 (t0)
REVERT: B  265 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7777 (pp)
REVERT: B  472 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7326 (mtm110)
REVERT: B  497 SER cc_start: 0.8204 (m) cc_final: 0.7959 (p)
REVERT: B  508 MET cc_start: 0.7624 (mmm) cc_final: 0.6439 (mtp)
REVERT: B  538 ASP cc_start: 0.7456 (t0) cc_final: 0.6865 (t0)
REVERT: B  549 GLU cc_start: 0.8354 (tt0) cc_final: 0.8140 (tt0)
REVERT: B  550 GLU cc_start: 0.7290 (pt0) cc_final: 0.6684 (pm20)
REVERT: B  608 ASN cc_start: 0.8743 (m-40) cc_final: 0.8476 (m110)
  outliers start: 9
  outliers final: 1
  residues processed: 126
  average time/residue: 0.9875
  time to fit residues: 132.0114
Evaluate side-chains
  107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  394 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   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 361 ASN
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.161103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.124572 restraints weight = 7076.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.51
r_work: 0.3147 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6796  Z= 0.225
  Angle     :  0.535   7.758   9202  Z= 0.289
  Chirality :  0.041   0.179    986
  Planarity :  0.004   0.041   1098
  Dihedral  : 12.437  64.547   1038
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.62 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.30), residues: 756
  helix:  1.95 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.38 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 395 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.022   0.002   PHE B 511 
 TYR   0.018   0.002   TYR A 352 
 ARG   0.003   0.000   ARG B 448 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A  376 LYS cc_start: 0.7853 (mttt) cc_final: 0.7366 (mmtm)
REVERT: A  471 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7899 (mmtm)
REVERT: A  523 CYS cc_start: 0.8814 (t) cc_final: 0.8495 (m)
REVERT: A  538 ASP cc_start: 0.8200 (t70) cc_final: 0.7607 (t0)
REVERT: A  622 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7940 (mt-10)
REVERT: B  265 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7713 (pp)
REVERT: B  301 LEU cc_start: 0.9291 (tp) cc_final: 0.9086 (tp)
REVERT: B  497 SER cc_start: 0.8330 (m) cc_final: 0.8017 (p)
REVERT: B  508 MET cc_start: 0.7703 (mmm) cc_final: 0.6541 (mtp)
REVERT: B  538 ASP cc_start: 0.7699 (t0) cc_final: 0.7151 (t0)
REVERT: B  549 GLU cc_start: 0.8428 (tt0) cc_final: 0.8196 (tt0)
REVERT: B  550 GLU cc_start: 0.7071 (pt0) cc_final: 0.6606 (pm20)
REVERT: B  577 ILE cc_start: 0.7393 (tt) cc_final: 0.7026 (pt)
REVERT: B  608 ASN cc_start: 0.8702 (m-40) cc_final: 0.8470 (m110)
  outliers start: 15
  outliers final: 5
  residues processed: 118
  average time/residue: 0.9099
  time to fit residues: 114.5490
Evaluate side-chains
  106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  447 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
A 576 GLN
B 310 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.157426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.119714 restraints weight = 7201.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.58
r_work: 0.3083 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6796  Z= 0.296
  Angle     :  0.568   6.994   9202  Z= 0.301
  Chirality :  0.042   0.186    986
  Planarity :  0.004   0.037   1098
  Dihedral  : 12.625  64.752   1036
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.54 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  1.25 (0.30), residues: 756
  helix:  1.81 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.32 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 395 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.018   0.002   PHE A 605 
 TYR   0.024   0.002   TYR A 496 
 ARG   0.003   0.000   ARG B 270 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A  376 LYS cc_start: 0.7964 (mttt) cc_final: 0.7473 (mmtm)
REVERT: A  471 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7942 (mmtm)
REVERT: A  523 CYS cc_start: 0.8968 (t) cc_final: 0.8592 (m)
REVERT: A  622 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8069 (mt-10)
REVERT: B  265 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7692 (pp)
REVERT: B  497 SER cc_start: 0.8393 (m) cc_final: 0.8022 (p)
REVERT: B  508 MET cc_start: 0.7776 (mmm) cc_final: 0.6559 (mtp)
REVERT: B  538 ASP cc_start: 0.7724 (t0) cc_final: 0.7163 (t0)
REVERT: B  549 GLU cc_start: 0.8459 (tt0) cc_final: 0.8176 (tt0)
REVERT: B  550 GLU cc_start: 0.7104 (pt0) cc_final: 0.6678 (pm20)
REVERT: B  577 ILE cc_start: 0.7688 (tt) cc_final: 0.7244 (pt)
  outliers start: 21
  outliers final: 7
  residues processed: 113
  average time/residue: 0.9010
  time to fit residues: 108.6983
Evaluate side-chains
  100 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   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 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.158431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.120725 restraints weight = 7261.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.60
r_work: 0.3096 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6796  Z= 0.265
  Angle     :  0.549   6.863   9202  Z= 0.293
  Chirality :  0.042   0.186    986
  Planarity :  0.004   0.039   1098
  Dihedral  : 12.482  64.801   1034
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.42 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  1.29 (0.30), residues: 756
  helix:  1.87 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.35 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 395 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.016   0.002   PHE B 610 
 TYR   0.025   0.002   TYR A 496 
 ARG   0.004   0.000   ARG B 270 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A  259 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6793 (tt)
REVERT: A  376 LYS cc_start: 0.7929 (mttt) cc_final: 0.7444 (mmtm)
REVERT: A  394 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7877 (t80)
REVERT: A  471 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7867 (mmtt)
REVERT: A  523 CYS cc_start: 0.8976 (t) cc_final: 0.8601 (m)
REVERT: A  622 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7990 (mt-10)
REVERT: B  265 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7712 (pp)
REVERT: B  472 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7148 (mtp85)
REVERT: B  497 SER cc_start: 0.8418 (m) cc_final: 0.7966 (p)
REVERT: B  508 MET cc_start: 0.7761 (mmm) cc_final: 0.6555 (mtp)
REVERT: B  538 ASP cc_start: 0.7735 (t0) cc_final: 0.7171 (t0)
REVERT: B  577 ILE cc_start: 0.7684 (tt) cc_final: 0.7186 (pt)
  outliers start: 18
  outliers final: 7
  residues processed: 113
  average time/residue: 0.9347
  time to fit residues: 112.8038
Evaluate side-chains
  106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0070
   chunk 53 optimal weight:    0.8980
   chunk 47 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
A 361 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.161115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.124826 restraints weight = 7216.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.52
r_work: 0.3151 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6796  Z= 0.194
  Angle     :  0.514   6.701   9202  Z= 0.276
  Chirality :  0.040   0.179    986
  Planarity :  0.004   0.038   1098
  Dihedral  : 12.257  64.020   1034
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.31 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  1.52 (0.30), residues: 756
  helix:  2.01 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.17 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 395 
 HIS   0.003   0.001   HIS B 313 
 PHE   0.017   0.001   PHE B 610 
 TYR   0.026   0.002   TYR A 496 
 ARG   0.004   0.000   ARG A 448 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A  376 LYS cc_start: 0.7792 (mttt) cc_final: 0.7296 (mmtm)
REVERT: A  394 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7770 (t80)
REVERT: A  470 THR cc_start: 0.8528 (m) cc_final: 0.8129 (p)
REVERT: A  471 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7851 (mmtt)
REVERT: A  523 CYS cc_start: 0.8863 (t) cc_final: 0.8506 (m)
REVERT: A  538 ASP cc_start: 0.8217 (t70) cc_final: 0.7514 (t0)
REVERT: B  265 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7659 (pp)
REVERT: B  394 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7824 (t80)
REVERT: B  472 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7046 (mtp85)
REVERT: B  497 SER cc_start: 0.8387 (m) cc_final: 0.7845 (p)
REVERT: B  508 MET cc_start: 0.7598 (mmm) cc_final: 0.6403 (mtp)
REVERT: B  538 ASP cc_start: 0.7693 (t0) cc_final: 0.7136 (t0)
REVERT: B  550 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6575 (pm20)
REVERT: B  577 ILE cc_start: 0.7565 (tt) cc_final: 0.7110 (pt)
  outliers start: 19
  outliers final: 5
  residues processed: 119
  average time/residue: 0.9677
  time to fit residues: 122.6978
Evaluate side-chains
  108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  550 GLU
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0670
   chunk 18 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.162531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.125553 restraints weight = 7114.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.57
r_work: 0.3157 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6796  Z= 0.209
  Angle     :  0.521   8.076   9202  Z= 0.278
  Chirality :  0.040   0.175    986
  Planarity :  0.004   0.038   1098
  Dihedral  : 12.227  63.932   1034
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.86 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  1.56 (0.30), residues: 756
  helix:  2.03 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.15 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 573 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.017   0.001   PHE B 610 
 TYR   0.028   0.002   TYR A 496 
 ARG   0.004   0.000   ARG A 448 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.625 
Fit side-chains
REVERT: A  376 LYS cc_start: 0.7877 (mttt) cc_final: 0.7406 (mmtm)
REVERT: A  394 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7826 (t80)
REVERT: A  470 THR cc_start: 0.8537 (m) cc_final: 0.8158 (p)
REVERT: A  471 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7890 (mmtt)
REVERT: A  523 CYS cc_start: 0.8922 (t) cc_final: 0.8568 (m)
REVERT: A  529 ASP cc_start: 0.8316 (m-30) cc_final: 0.7942 (m-30)
REVERT: B  265 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7736 (pp)
REVERT: B  394 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7799 (t80)
REVERT: B  472 ARG cc_start: 0.7600 (mtm110) cc_final: 0.7071 (mtp85)
REVERT: B  497 SER cc_start: 0.8391 (m) cc_final: 0.7842 (p)
REVERT: B  508 MET cc_start: 0.7635 (mmm) cc_final: 0.6435 (mtp)
REVERT: B  538 ASP cc_start: 0.7706 (t0) cc_final: 0.7138 (t0)
REVERT: B  550 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6745 (pm20)
REVERT: B  577 ILE cc_start: 0.7658 (tt) cc_final: 0.7175 (pt)
  outliers start: 17
  outliers final: 9
  residues processed: 115
  average time/residue: 0.9081
  time to fit residues: 111.6884
Evaluate side-chains
  110 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  550 GLU
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 73 optimal weight:    0.1980
   chunk 2 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   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 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.161539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.125292 restraints weight = 7179.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.50
r_work: 0.3156 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6796  Z= 0.203
  Angle     :  0.517   8.050   9202  Z= 0.276
  Chirality :  0.040   0.204    986
  Planarity :  0.004   0.038   1098
  Dihedral  : 12.192  63.203   1034
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.45 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.30), residues: 756
  helix:  2.06 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.11 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 573 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.017   0.001   PHE B 610 
 TYR   0.029   0.002   TYR A 496 
 ARG   0.004   0.000   ARG A 448 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  376 LYS cc_start: 0.7790 (mttt) cc_final: 0.7293 (mmtm)
REVERT: A  394 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7748 (t80)
REVERT: A  470 THR cc_start: 0.8505 (m) cc_final: 0.8087 (p)
REVERT: A  471 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7986 (mmtt)
REVERT: A  523 CYS cc_start: 0.8871 (t) cc_final: 0.8495 (m)
REVERT: A  529 ASP cc_start: 0.8277 (m-30) cc_final: 0.7894 (m-30)
REVERT: B  265 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7674 (pp)
REVERT: B  394 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7786 (t80)
REVERT: B  472 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7112 (mtp85)
REVERT: B  497 SER cc_start: 0.8348 (m) cc_final: 0.7791 (p)
REVERT: B  508 MET cc_start: 0.7633 (mmm) cc_final: 0.6428 (mtp)
REVERT: B  538 ASP cc_start: 0.7668 (t0) cc_final: 0.7092 (t0)
REVERT: B  577 ILE cc_start: 0.7611 (tt) cc_final: 0.7119 (pt)
  outliers start: 18
  outliers final: 8
  residues processed: 112
  average time/residue: 0.8747
  time to fit residues: 104.7730
Evaluate side-chains
  108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 69 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.161862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.124726 restraints weight = 7113.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.56
r_work: 0.3123 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6796  Z= 0.214
  Angle     :  0.523   8.006   9202  Z= 0.279
  Chirality :  0.041   0.226    986
  Planarity :  0.004   0.040   1098
  Dihedral  : 12.162  63.114   1034
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.90 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  1.53 (0.30), residues: 756
  helix:  1.93 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -2.21 (0.42), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 573 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.016   0.001   PHE B 610 
 TYR   0.029   0.002   TYR A 496 
 ARG   0.003   0.000   ARG B 270 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LYS cc_start: 0.7876 (mttt) cc_final: 0.7405 (mmtm)
REVERT: A  394 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7819 (t80)
REVERT: A  470 THR cc_start: 0.8479 (m) cc_final: 0.8077 (p)
REVERT: A  471 LYS cc_start: 0.8205 (mmtt) cc_final: 0.8003 (mmtt)
REVERT: A  523 CYS cc_start: 0.8922 (t) cc_final: 0.8573 (m)
REVERT: A  529 ASP cc_start: 0.8307 (m-30) cc_final: 0.7933 (m-30)
REVERT: B  265 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7742 (pp)
REVERT: B  394 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7861 (t80)
REVERT: B  472 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7222 (mtp85)
REVERT: B  497 SER cc_start: 0.8339 (m) cc_final: 0.7744 (p)
REVERT: B  508 MET cc_start: 0.7658 (mmm) cc_final: 0.6466 (mtp)
REVERT: B  538 ASP cc_start: 0.7728 (t0) cc_final: 0.7160 (t0)
REVERT: B  577 ILE cc_start: 0.7664 (tt) cc_final: 0.7158 (pt)
  outliers start: 17
  outliers final: 9
  residues processed: 112
  average time/residue: 0.9167
  time to fit residues: 109.7894
Evaluate side-chains
  108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  550 GLU
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 1 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 15 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 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.160595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.123188 restraints weight = 7215.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.57
r_work: 0.3130 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6796  Z= 0.201
  Angle     :  0.518   7.956   9202  Z= 0.277
  Chirality :  0.040   0.251    986
  Planarity :  0.004   0.040   1098
  Dihedral  : 12.090  62.781   1034
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.34 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  1.57 (0.30), residues: 756
  helix:  1.94 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -2.13 (0.43), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 573 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.017   0.001   PHE B 610 
 TYR   0.028   0.002   TYR B 496 
 ARG   0.005   0.000   ARG B 270 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LYS cc_start: 0.7852 (mttt) cc_final: 0.7365 (mmtm)
REVERT: A  394 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7805 (t80)
REVERT: A  413 MET cc_start: 0.7803 (mtp) cc_final: 0.7415 (ttt)
REVERT: A  470 THR cc_start: 0.8410 (m) cc_final: 0.7923 (p)
REVERT: A  472 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7726 (mtp180)
REVERT: A  523 CYS cc_start: 0.8917 (t) cc_final: 0.8568 (m)
REVERT: A  538 ASP cc_start: 0.8298 (t70) cc_final: 0.7604 (t0)
REVERT: B  265 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7686 (pp)
REVERT: B  394 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7849 (t80)
REVERT: B  472 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7239 (mtp85)
REVERT: B  497 SER cc_start: 0.8326 (m) cc_final: 0.7722 (p)
REVERT: B  508 MET cc_start: 0.7621 (mmm) cc_final: 0.6436 (mtp)
REVERT: B  538 ASP cc_start: 0.7729 (t0) cc_final: 0.7159 (t0)
REVERT: B  577 ILE cc_start: 0.7638 (tt) cc_final: 0.7155 (pt)
  outliers start: 12
  outliers final: 8
  residues processed: 106
  average time/residue: 0.9726
  time to fit residues: 110.0750
Evaluate side-chains
  110 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  550 GLU
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 2 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 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.159405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.121829 restraints weight = 7261.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.59
r_work: 0.3110 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6796  Z= 0.256
  Angle     :  0.550   7.843   9202  Z= 0.293
  Chirality :  0.042   0.251    986
  Planarity :  0.004   0.041   1098
  Dihedral  : 12.215  63.606   1034
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.78 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  1.41 (0.30), residues: 756
  helix:  1.81 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -2.15 (0.43), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 573 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.016   0.002   PHE B 610 
 TYR   0.026   0.002   TYR B 496 
 ARG   0.005   0.000   ARG B 270 

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LYS cc_start: 0.7891 (mttt) cc_final: 0.7410 (mmtm)
REVERT: A  394 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7869 (t80)
REVERT: A  413 MET cc_start: 0.7843 (mtp) cc_final: 0.7482 (ttt)
REVERT: A  470 THR cc_start: 0.8416 (m) cc_final: 0.7921 (p)
REVERT: A  472 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7747 (mtp180)
REVERT: A  523 CYS cc_start: 0.8938 (t) cc_final: 0.8573 (m)
REVERT: A  538 ASP cc_start: 0.8302 (t70) cc_final: 0.7604 (t0)
REVERT: B  265 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7652 (pp)
REVERT: B  394 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7810 (t80)
REVERT: B  472 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7210 (mtp85)
REVERT: B  497 SER cc_start: 0.8333 (m) cc_final: 0.7736 (p)
REVERT: B  508 MET cc_start: 0.7662 (mmm) cc_final: 0.6447 (mtp)
REVERT: B  538 ASP cc_start: 0.7735 (t0) cc_final: 0.7152 (t0)
REVERT: B  577 ILE cc_start: 0.7668 (tt) cc_final: 0.7141 (pt)
  outliers start: 14
  outliers final: 8
  residues processed: 106
  average time/residue: 0.9689
  time to fit residues: 109.1951
Evaluate side-chains
  104 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  550 GLU
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 35 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 10 optimal weight:    0.2980
   chunk 72 optimal weight:    0.0980
   chunk 62 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.162652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.127653 restraints weight = 7250.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.53
r_work: 0.3163 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6796  Z= 0.186
  Angle     :  0.516   7.873   9202  Z= 0.277
  Chirality :  0.040   0.247    986
  Planarity :  0.004   0.040   1098
  Dihedral  : 12.020  59.963   1034
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.49 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  1.59 (0.30), residues: 756
  helix:  1.94 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -2.08 (0.44), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 573 
 HIS   0.003   0.001   HIS B 313 
 PHE   0.017   0.001   PHE B 610 
 TYR   0.024   0.002   TYR A 496 
 ARG   0.005   0.000   ARG B 270 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4865.43 seconds
wall clock time: 83 minutes 38.78 seconds (5018.78 seconds total)