Starting phenix.real_space_refine
on Sat May 10 16:33:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j51_61139/05_2025/9j51_61139.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j51_61139/05_2025/9j51_61139.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j51_61139/05_2025/9j51_61139.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j51_61139/05_2025/9j51_61139.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j51_61139/05_2025/9j51_61139.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j51_61139/05_2025/9j51_61139.cif"
  }
  resolution = 3.1
  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=  -0.001 sd=   0.075
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       5      5.49       5
     S      30      5.16       5
     C    4454      2.51       5
     N    1022      2.21       5
     O    1070      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-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6581
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3174
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 13, 'TRANS': 366}
          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: {'PTRANS': 14, 'TRANS': 367}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 113
          Unusual residues: {'PC1': 2, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    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: 4.62, per 1000 atoms: 0.70
  Number of scatterers: 6581
  At special positions: 0
  Unit cell: (126.26, 67.41, 74.9, 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       5     15.00
     O    1070      8.00
     N    1022      7.00
     C    4454      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 818.2 milliseconds
  

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1448

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 0 sheets defined
      77.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 231 through 258
      removed outlier: 4.067A  pdb=" N   GLY A 242 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   ILE A 245 " --> pdb=" O   CYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 4.237A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.619A  pdb=" N   PHE A 303 " --> pdb=" O   HIS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 336
    Processing helix  chain 'A' and resid 337 through 340
    Processing helix  chain 'A' and resid 345 through 360
      removed outlier: 4.486A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
      removed outlier: 3.600A  pdb=" N   THR A 383 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.744A  pdb=" N   ASN A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 4.278A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 471
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 472 through 502
      removed outlier: 4.021A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 478 " --> pdb=" O   PHE A 474 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   ASN A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 3.563A  pdb=" N   PHE A 510 " --> pdb=" O   ASP A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 545
      removed outlier: 3.505A  pdb=" N   THR A 545 " --> pdb=" O   GLY A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 580
      removed outlier: 3.541A  pdb=" N   TYR A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 618
      removed outlier: 3.682A  pdb=" N   ALA A 593 " --> pdb=" O   GLY A 589 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 3.904A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 258
      removed outlier: 3.574A  pdb=" N   VAL B 256 " --> pdb=" O   VAL B 252 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE B 257 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 3.874A  pdb=" N   ILE B 271 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 337
    Processing helix  chain 'B' and resid 346 through 360
    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: 3.656A  pdb=" N   ASN B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   SER B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   VAL B 405 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ILE B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 452
    Processing helix  chain 'B' and resid 453 through 462
    Processing helix  chain 'B' and resid 464 through 471
      removed outlier: 3.652A  pdb=" N   ASP B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 472 through 502
      removed outlier: 3.899A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   VAL B 478 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG B 502 " --> pdb=" O   THR B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.532A  pdb=" N   PHE B 510 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 582
      removed outlier: 3.953A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ALA B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR B 582 " --> pdb=" O   SER B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 617
      removed outlier: 3.755A  pdb=" N   ALA B 593 " --> pdb=" O   GLY B 589 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 3.703A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU B 612 " --> pdb=" O   ASN B 608 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU B 613 " --> pdb=" O   PHE B 609 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1263 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: 1.64

  Time building geometry restraints manager: 2.01 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: 1010
        1.32 -     1.45: 2045
        1.45 -     1.57: 3682
        1.57 -     1.69: 8
        1.69 -     1.82: 42
  Bond restraints: 6787
  Sorted by residual:
  bond pdb=" C   THR A 582 "
       pdb=" O   THR A 582 "
    ideal  model  delta    sigma   weight residual
    1.236  1.252 -0.015 7.30e-03 1.88e+04 4.36e+00
  bond pdb=" CA  ILE B 454 "
       pdb=" CB  ILE B 454 "
    ideal  model  delta    sigma   weight residual
    1.539  1.529  0.010 5.40e-03 3.43e+04 3.73e+00
  bond pdb=" CA  ILE A 360 "
       pdb=" C   ILE A 360 "
    ideal  model  delta    sigma   weight residual
    1.524  1.515  0.009 8.60e-03 1.35e+04 1.18e+00
  bond pdb=" C   ALA A 597 "
       pdb=" N   PRO A 598 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.014 1.28e-02 6.10e+03 1.14e+00
  bond pdb=" N   ARG B 624 "
       pdb=" CA  ARG B 624 "
    ideal  model  delta    sigma   weight residual
    1.458  1.478 -0.020 1.90e-02 2.77e+03 1.14e+00
  ... (remaining 6782 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 8914
        1.37 -     2.74: 222
        2.74 -     4.12: 36
        4.12 -     5.49: 15
        5.49 -     6.86: 2
  Bond angle restraints: 9189
  Sorted by residual:
  angle pdb=" C   CYS A 453 "
        pdb=" N   ILE A 454 "
        pdb=" CA  ILE A 454 "
      ideal   model   delta    sigma   weight residual
     120.33  123.55   -3.22 8.00e-01 1.56e+00 1.62e+01
  angle pdb=" C   PHE B 623 "
        pdb=" N   ARG B 624 "
        pdb=" CA  ARG B 624 "
      ideal   model   delta    sigma   weight residual
     121.70  128.56   -6.86 1.80e+00 3.09e-01 1.45e+01
  angle pdb=" CA  LEU B 617 "
        pdb=" C   LEU B 617 "
        pdb=" N   ASN B 618 "
      ideal   model   delta    sigma   weight residual
     117.79  113.59    4.20 1.22e+00 6.72e-01 1.19e+01
  angle pdb=" N   GLY B 621 "
        pdb=" CA  GLY B 621 "
        pdb=" C   GLY B 621 "
      ideal   model   delta    sigma   weight residual
     114.64  110.11    4.53 1.40e+00 5.10e-01 1.05e+01
  angle pdb=" N   VAL B 346 "
        pdb=" CA  VAL B 346 "
        pdb=" C   VAL B 346 "
      ideal   model   delta    sigma   weight residual
     113.39  109.12    4.27 1.47e+00 4.63e-01 8.44e+00
  ... (remaining 9184 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 3506
       17.36 -    34.72: 296
       34.72 -    52.08: 81
       52.08 -    69.44: 24
       69.44 -    86.81: 2
  Dihedral angle restraints: 3909
    sinusoidal: 1665
      harmonic: 2244
  Sorted by residual:
  dihedral pdb=" CA  ALA A 384 "
           pdb=" C   ALA A 384 "
           pdb=" N   PRO A 385 "
           pdb=" CA  PRO A 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.25   25.75     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  GLY A 242 "
           pdb=" C   GLY A 242 "
           pdb=" N   ILE A 243 "
           pdb=" CA  ILE A 243 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.91   20.09     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CA  ASP B 538 "
           pdb=" CB  ASP B 538 "
           pdb=" CG  ASP B 538 "
           pdb=" OD1 ASP B 538 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.01   56.01     1      2.00e+01 2.50e-03 1.06e+01
  ... (remaining 3906 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 533
       0.025 -    0.050: 279
       0.050 -    0.075: 117
       0.075 -    0.100: 39
       0.100 -    0.125: 16
  Chirality restraints: 984
  Sorted by residual:
  chirality pdb=" CB  VAL B 567 "
            pdb=" CA  VAL B 567 "
            pdb=" CG1 VAL B 567 "
            pdb=" CG2 VAL B 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 3.92e-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   -0.12 2.00e-01 2.50e+01 3.89e-01
  chirality pdb=" CA  TRP B 266 "
            pdb=" N   TRP B 266 "
            pdb=" C   TRP B 266 "
            pdb=" CB  TRP B 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 981 not shown)

  Planarity restraints: 1095
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 242 "    0.012 2.00e-02 2.50e+03   2.30e-02 5.31e+00
        pdb=" C   GLY A 242 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   GLY A 242 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ILE A 243 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 384 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.19e+00
        pdb=" N   PRO A 385 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 385 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 385 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 460 "    0.010 2.00e-02 2.50e+03   9.01e-03 1.42e+00
        pdb=" CG  PHE A 460 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 460 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 460 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 460 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 460 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 460 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1092 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 92
        2.65 -     3.22: 6358
        3.22 -     3.78: 10583
        3.78 -     4.34: 14411
        4.34 -     4.90: 23475
  Nonbonded interactions: 54919
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 482 "
            pdb=" OG1 THR A 485 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   ILE B 271 "
            pdb=" OH  TYR B 352 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" O   LYS B 482 "
            pdb=" OG1 THR B 485 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   GLN A 576 "
            pdb=" OG1 THR A 580 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER A 370 "
            pdb=" O14 PC1 A 801 "
     model   vdw
     2.240 3.040
  ... (remaining 54914 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 231 through 624 or resid 801 through 802))
  selection = (chain 'B' and (resid 231 through 624 or resid 801 through 802))
}

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:             2.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     18.570
  Find NCS groups from input model:        0.260
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
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   6788  Z= 0.154
  Angle     :  0.547   6.861   9189  Z= 0.314
  Chirality :  0.038   0.125    984
  Planarity :  0.004   0.051   1095
  Dihedral  : 14.554  86.805   2461
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  :  8.12 %
    Favored  : 89.22 %
  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 (0.31), residues: 754
  helix:  1.43 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -3.02 (0.41), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 607 
 HIS   0.004   0.001   HIS B 616 
 PHE   0.021   0.001   PHE A 460 
 TYR   0.012   0.001   TYR B 518 
 ARG   0.003   0.000   ARG A 570 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12625 (  424)
  hydrogen bonds       : angle       5.33542 ( 1263)
  covalent geometry    : bond        0.00314 ( 6787)
  covalent geometry    : angle       0.54669 ( 9189)
  Misc. bond           : bond        0.00020 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.8204 (mmm) cc_final: 0.7798 (mmm)
REVERT: A  488 PHE cc_start: 0.8141 (m-80) cc_final: 0.7769 (m-80)
REVERT: A  504 HIS cc_start: 0.7560 (t-90) cc_final: 0.7239 (t-170)
REVERT: A  508 MET cc_start: 0.7767 (mmm) cc_final: 0.7428 (mmm)
REVERT: A  511 PHE cc_start: 0.8307 (t80) cc_final: 0.8091 (t80)
REVERT: A  528 TRP cc_start: 0.8360 (t-100) cc_final: 0.8116 (t-100)
REVERT: B  280 GLU cc_start: 0.8722 (tt0) cc_final: 0.8327 (tt0)
REVERT: B  283 PHE cc_start: 0.6853 (t80) cc_final: 0.6561 (t80)
REVERT: B  413 MET cc_start: 0.5761 (mtp) cc_final: 0.5446 (mtm)
REVERT: B  517 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7695 (m-80)
REVERT: B  556 LYS cc_start: 0.7767 (mppt) cc_final: 0.7115 (mtpt)
REVERT: B  615 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6903 (tm-30)
REVERT: B  624 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.5096 (mmp80)
  outliers start: 18
  outliers final: 8
  residues processed: 172
  average time/residue: 0.1903
  time to fit residues: 42.6687
Evaluate side-chains
  134 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  618 ASN
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  517 PHE
Chi-restraints excluded: chain B residue  624 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0000
   chunk 38 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 69 optimal weight:    0.4980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
A 540 ASN
B 294 GLN
B 387 HIS
B 399 GLN
B 608 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.186373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.158146 restraints weight = 8927.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 2.16
r_work: 0.3683 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6788  Z= 0.144
  Angle     :  0.552   8.630   9189  Z= 0.296
  Chirality :  0.040   0.134    984
  Planarity :  0.004   0.049   1095
  Dihedral  : 11.554  60.497   1050
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 12.11 %
    Favored  : 85.08 %
  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 (0.31), residues: 754
  helix:  1.38 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -2.97 (0.41), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 607 
 HIS   0.003   0.001   HIS A 499 
 PHE   0.022   0.001   PHE B 394 
 TYR   0.013   0.002   TYR B 518 
 ARG   0.005   0.001   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04528 (  424)
  hydrogen bonds       : angle       4.49359 ( 1263)
  covalent geometry    : bond        0.00318 ( 6787)
  covalent geometry    : angle       0.55170 ( 9189)
  Misc. bond           : bond        0.00085 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.8223 (mmm) cc_final: 0.7449 (mmm)
REVERT: A  488 PHE cc_start: 0.8232 (m-80) cc_final: 0.7751 (m-80)
REVERT: A  504 HIS cc_start: 0.7566 (t-90) cc_final: 0.7142 (t-170)
REVERT: A  511 PHE cc_start: 0.8303 (t80) cc_final: 0.8045 (t80)
REVERT: A  528 TRP cc_start: 0.8416 (t-100) cc_final: 0.8080 (t-100)
REVERT: B  283 PHE cc_start: 0.6711 (t80) cc_final: 0.6450 (t80)
REVERT: B  409 ASP cc_start: 0.7552 (m-30) cc_final: 0.7222 (m-30)
REVERT: B  413 MET cc_start: 0.5521 (mtp) cc_final: 0.5146 (mtp)
REVERT: B  508 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6533 (ppp)
REVERT: B  517 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7552 (m-10)
REVERT: B  556 LYS cc_start: 0.7654 (mppt) cc_final: 0.6963 (mtpt)
REVERT: B  615 GLU cc_start: 0.7547 (tm-30) cc_final: 0.6936 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 150
  average time/residue: 0.1823
  time to fit residues: 36.5388
Evaluate side-chains
  136 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  508 MET
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  517 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 248 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.184637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.156264 restraints weight = 8905.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 2.15
r_work: 0.3662 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6788  Z= 0.152
  Angle     :  0.551   7.479   9189  Z= 0.291
  Chirality :  0.040   0.130    984
  Planarity :  0.004   0.052   1095
  Dihedral  : 11.492  61.806   1040
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.70 %
    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:  0.35 (0.31), residues: 754
  helix:  1.30 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -2.89 (0.42), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 607 
 HIS   0.003   0.001   HIS A 499 
 PHE   0.024   0.001   PHE B 394 
 TYR   0.018   0.002   TYR A 412 
 ARG   0.004   0.000   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04432 (  424)
  hydrogen bonds       : angle       4.39429 ( 1263)
  covalent geometry    : bond        0.00343 ( 6787)
  covalent geometry    : angle       0.55120 ( 9189)
  Misc. bond           : bond        0.00081 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 TYR cc_start: 0.8145 (m-80) cc_final: 0.7832 (m-80)
REVERT: A  488 PHE cc_start: 0.8236 (m-80) cc_final: 0.7794 (m-80)
REVERT: A  504 HIS cc_start: 0.7626 (t-90) cc_final: 0.7337 (t-170)
REVERT: A  511 PHE cc_start: 0.8380 (t80) cc_final: 0.8142 (t80)
REVERT: A  528 TRP cc_start: 0.8390 (t-100) cc_final: 0.7966 (t-100)
REVERT: B  283 PHE cc_start: 0.6791 (t80) cc_final: 0.6364 (t80)
REVERT: B  409 ASP cc_start: 0.7594 (m-30) cc_final: 0.7328 (m-30)
REVERT: B  413 MET cc_start: 0.5247 (mtp) cc_final: 0.5037 (mtp)
REVERT: B  517 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7706 (m-80)
REVERT: B  615 GLU cc_start: 0.7488 (tm-30) cc_final: 0.6915 (tm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 153
  average time/residue: 0.1673
  time to fit residues: 34.4406
Evaluate side-chains
  137 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  517 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0000
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** B 399 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 = 0.4123 r_free = 0.4123 target = 0.185493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.157340 restraints weight = 9015.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 2.16
r_work: 0.3675 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6788  Z= 0.135
  Angle     :  0.547   8.475   9189  Z= 0.286
  Chirality :  0.040   0.219    984
  Planarity :  0.004   0.047   1095
  Dihedral  : 11.411  61.973   1040
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.03 %
    Favored  : 83.01 %
  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:  0.46 (0.31), residues: 754
  helix:  1.38 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -2.82 (0.42), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 514 
 HIS   0.003   0.001   HIS A 499 
 PHE   0.026   0.001   PHE B 394 
 TYR   0.018   0.002   TYR B 290 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  424)
  hydrogen bonds       : angle       4.35631 ( 1263)
  covalent geometry    : bond        0.00300 ( 6787)
  covalent geometry    : angle       0.54748 ( 9189)
  Misc. bond           : bond        0.00088 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 TYR cc_start: 0.8148 (m-80) cc_final: 0.7912 (m-80)
REVERT: A  488 PHE cc_start: 0.8224 (m-80) cc_final: 0.7791 (m-80)
REVERT: A  496 TYR cc_start: 0.8381 (t80) cc_final: 0.8127 (t80)
REVERT: A  504 HIS cc_start: 0.7740 (t-90) cc_final: 0.7396 (t-170)
REVERT: A  511 PHE cc_start: 0.8340 (t80) cc_final: 0.8137 (t80)
REVERT: A  512 TYR cc_start: 0.8258 (m-10) cc_final: 0.7686 (m-10)
REVERT: A  528 TRP cc_start: 0.8395 (t-100) cc_final: 0.8027 (t-100)
REVERT: B  283 PHE cc_start: 0.6783 (t80) cc_final: 0.6360 (t80)
REVERT: B  517 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7591 (m-10)
REVERT: B  615 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7071 (tm-30)
  outliers start: 20
  outliers final: 17
  residues processed: 150
  average time/residue: 0.1638
  time to fit residues: 33.4812
Evaluate side-chains
  143 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  517 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 53 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0970
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
B 608 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.187150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.158651 restraints weight = 8910.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 2.18
r_work: 0.3695 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6788  Z= 0.124
  Angle     :  0.541   8.606   9189  Z= 0.281
  Chirality :  0.040   0.207    984
  Planarity :  0.004   0.049   1095
  Dihedral  : 11.293  61.209   1040
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.33 %
    Favored  : 82.42 %
  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:  0.63 (0.31), residues: 754
  helix:  1.53 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -2.78 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 514 
 HIS   0.003   0.001   HIS A 499 
 PHE   0.027   0.001   PHE B 394 
 TYR   0.018   0.002   TYR B 290 
 ARG   0.003   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04149 (  424)
  hydrogen bonds       : angle       4.31184 ( 1263)
  covalent geometry    : bond        0.00268 ( 6787)
  covalent geometry    : angle       0.54075 ( 9189)
  Misc. bond           : bond        0.00090 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 TYR cc_start: 0.8172 (m-80) cc_final: 0.7961 (m-80)
REVERT: A  488 PHE cc_start: 0.8219 (m-80) cc_final: 0.7789 (m-80)
REVERT: A  504 HIS cc_start: 0.7733 (t-90) cc_final: 0.7373 (t-170)
REVERT: A  512 TYR cc_start: 0.8300 (m-10) cc_final: 0.7691 (m-10)
REVERT: A  528 TRP cc_start: 0.8400 (t-100) cc_final: 0.7991 (t-100)
REVERT: A  532 MET cc_start: 0.6863 (mmt) cc_final: 0.6644 (mmt)
REVERT: B  283 PHE cc_start: 0.6662 (t80) cc_final: 0.6278 (t80)
REVERT: B  517 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7556 (m-80)
REVERT: B  615 GLU cc_start: 0.7541 (tm-30) cc_final: 0.6957 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 152
  average time/residue: 0.1512
  time to fit residues: 31.6716
Evaluate side-chains
  143 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  517 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 35 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 11 optimal weight:    0.2980
   chunk 60 optimal weight:    0.0970
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
B 399 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.187744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.159552 restraints weight = 8816.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 2.16
r_work: 0.3711 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6788  Z= 0.122
  Angle     :  0.547   7.737   9189  Z= 0.285
  Chirality :  0.040   0.218    984
  Planarity :  0.004   0.043   1095
  Dihedral  : 11.148  60.464   1040
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 15.51 %
    Favored  : 81.24 %
  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:  0.73 (0.32), residues: 754
  helix:  1.59 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -2.70 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 514 
 HIS   0.003   0.001   HIS A 499 
 PHE   0.027   0.001   PHE B 394 
 TYR   0.021   0.002   TYR A 496 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04118 (  424)
  hydrogen bonds       : angle       4.29978 ( 1263)
  covalent geometry    : bond        0.00264 ( 6787)
  covalent geometry    : angle       0.54710 ( 9189)
  Misc. bond           : bond        0.00089 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  488 PHE cc_start: 0.8197 (m-80) cc_final: 0.7781 (m-80)
REVERT: A  511 PHE cc_start: 0.8196 (t80) cc_final: 0.7973 (t80)
REVERT: A  528 TRP cc_start: 0.8358 (t-100) cc_final: 0.7967 (t-100)
REVERT: A  532 MET cc_start: 0.6883 (mmt) cc_final: 0.6670 (mmt)
REVERT: B  283 PHE cc_start: 0.6608 (t80) cc_final: 0.6267 (t80)
REVERT: B  401 ASN cc_start: 0.7679 (m110) cc_final: 0.7452 (m110)
REVERT: B  517 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7510 (m-10)
REVERT: B  615 GLU cc_start: 0.7511 (tm-30) cc_final: 0.6956 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 146
  average time/residue: 0.1650
  time to fit residues: 33.8308
Evaluate side-chains
  142 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  517 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 61 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.185340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.156949 restraints weight = 9013.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 2.13
r_work: 0.3686 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6788  Z= 0.155
  Angle     :  0.565   7.514   9189  Z= 0.294
  Chirality :  0.041   0.230    984
  Planarity :  0.004   0.050   1095
  Dihedral  : 11.398  61.808   1039
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 15.81 %
    Favored  : 80.95 %
  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 (0.31), residues: 754
  helix:  1.39 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -2.71 (0.44), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 514 
 HIS   0.003   0.001   HIS A 499 
 PHE   0.026   0.001   PHE B 394 
 TYR   0.023   0.002   TYR B 290 
 ARG   0.003   0.000   ARG A 570 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04342 (  424)
  hydrogen bonds       : angle       4.36561 ( 1263)
  covalent geometry    : bond        0.00356 ( 6787)
  covalent geometry    : angle       0.56470 ( 9189)
  Misc. bond           : bond        0.00076 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
REVERT: A  488 PHE cc_start: 0.8214 (m-80) cc_final: 0.7838 (m-80)
REVERT: A  511 PHE cc_start: 0.8330 (t80) cc_final: 0.8085 (t80)
REVERT: A  512 TYR cc_start: 0.8210 (m-10) cc_final: 0.7645 (m-10)
REVERT: A  528 TRP cc_start: 0.8280 (t-100) cc_final: 0.7908 (t-100)
REVERT: B  283 PHE cc_start: 0.6869 (t80) cc_final: 0.6503 (t80)
REVERT: B  517 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7634 (m-80)
REVERT: B  615 GLU cc_start: 0.7483 (tm-30) cc_final: 0.6996 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 147
  average time/residue: 0.1521
  time to fit residues: 31.2314
Evaluate side-chains
  142 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  517 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0000
   chunk 68 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 504 HIS
B 616 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.186804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.158678 restraints weight = 8944.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 2.11
r_work: 0.3702 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6788  Z= 0.132
  Angle     :  0.561   8.093   9189  Z= 0.293
  Chirality :  0.040   0.199    984
  Planarity :  0.004   0.046   1095
  Dihedral  : 11.331  61.656   1039
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.99 %
    Favored  : 80.06 %
  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 (0.31), residues: 754
  helix:  1.45 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -2.63 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 514 
 HIS   0.006   0.001   HIS A 504 
 PHE   0.029   0.001   PHE B 394 
 TYR   0.020   0.002   TYR B 290 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04240 (  424)
  hydrogen bonds       : angle       4.36317 ( 1263)
  covalent geometry    : bond        0.00296 ( 6787)
  covalent geometry    : angle       0.56126 ( 9189)
  Misc. bond           : bond        0.00086 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  488 PHE cc_start: 0.8191 (m-80) cc_final: 0.7815 (m-80)
REVERT: A  511 PHE cc_start: 0.8315 (t80) cc_final: 0.8092 (t80)
REVERT: A  528 TRP cc_start: 0.8296 (t-100) cc_final: 0.7887 (t-100)
REVERT: B  283 PHE cc_start: 0.6807 (t80) cc_final: 0.6427 (t80)
REVERT: B  517 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7556 (m-10)
REVERT: B  615 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6985 (tm-30)
  outliers start: 20
  outliers final: 19
  residues processed: 147
  average time/residue: 0.1705
  time to fit residues: 34.5546
Evaluate side-chains
  143 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  517 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 54 optimal weight:    0.0870
   chunk 68 optimal weight:    0.0010
   chunk 56 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0060
   chunk 21 optimal weight:    0.1980
   chunk 46 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 10 optimal weight:    0.2980
   chunk 29 optimal weight:    0.0040
   chunk 69 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.0592

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

Flipped N/Q/H residues before XYZ refinement:
A 476 HIS
A 504 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.193102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.165730 restraints weight = 8934.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 2.10
r_work: 0.3774 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6788  Z= 0.114
  Angle     :  0.553   8.157   9189  Z= 0.289
  Chirality :  0.040   0.206    984
  Planarity :  0.004   0.043   1095
  Dihedral  : 10.734  59.385   1039
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.73 %
    Favored  : 79.76 %
  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:  0.94 (0.32), residues: 754
  helix:  1.74 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -2.60 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 514 
 HIS   0.006   0.001   HIS A 504 
 PHE   0.029   0.001   PHE B 394 
 TYR   0.017   0.001   TYR B 290 
 ARG   0.006   0.000   ARG B 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03918 (  424)
  hydrogen bonds       : angle       4.22116 ( 1263)
  covalent geometry    : bond        0.00231 ( 6787)
  covalent geometry    : angle       0.55275 ( 9189)
  Misc. bond           : bond        0.00110 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  488 PHE cc_start: 0.8235 (m-80) cc_final: 0.7868 (m-80)
REVERT: A  500 LYS cc_start: 0.6997 (tttp) cc_final: 0.6789 (ttmm)
REVERT: A  508 MET cc_start: 0.7178 (mmm) cc_final: 0.6396 (tpp)
REVERT: A  511 PHE cc_start: 0.8272 (t80) cc_final: 0.8008 (t80)
REVERT: A  528 TRP cc_start: 0.8247 (t-100) cc_final: 0.7869 (t-100)
REVERT: B  283 PHE cc_start: 0.6473 (t80) cc_final: 0.6207 (t80)
REVERT: B  472 ARG cc_start: 0.7130 (mmm-85) cc_final: 0.6041 (tpp-160)
REVERT: B  517 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7763 (m-10)
REVERT: B  520 ILE cc_start: 0.6587 (tp) cc_final: 0.6363 (tp)
REVERT: B  615 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6928 (tm-30)
  outliers start: 17
  outliers final: 15
  residues processed: 160
  average time/residue: 0.1645
  time to fit residues: 36.1538
Evaluate side-chains
  150 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  517 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0670
   chunk 0 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6920

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.187585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.159619 restraints weight = 9083.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 2.10
r_work: 0.3705 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6788  Z= 0.154
  Angle     :  0.603   7.764   9189  Z= 0.317
  Chirality :  0.042   0.195    984
  Planarity :  0.004   0.045   1095
  Dihedral  : 11.119  59.947   1038
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.91 %
    Favored  : 78.58 %
  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:  0.65 (0.31), residues: 754
  helix:  1.49 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -2.59 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 514 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.029   0.001   PHE B 394 
 TYR   0.027   0.002   TYR B 290 
 ARG   0.006   0.000   ARG B 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04339 (  424)
  hydrogen bonds       : angle       4.39152 ( 1263)
  covalent geometry    : bond        0.00356 ( 6787)
  covalent geometry    : angle       0.60274 ( 9189)
  Misc. bond           : bond        0.00069 (    1)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  488 PHE cc_start: 0.8291 (m-80) cc_final: 0.7975 (m-80)
REVERT: A  528 TRP cc_start: 0.8334 (t-100) cc_final: 0.7919 (t-100)
REVERT: B  283 PHE cc_start: 0.6766 (t80) cc_final: 0.6523 (t80)
REVERT: B  472 ARG cc_start: 0.7313 (mmm-85) cc_final: 0.6181 (tpp-160)
REVERT: B  517 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7670 (m-10)
REVERT: B  520 ILE cc_start: 0.6734 (tp) cc_final: 0.6458 (tp)
REVERT: B  615 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6974 (tm-30)
  outliers start: 17
  outliers final: 16
  residues processed: 139
  average time/residue: 0.1643
  time to fit residues: 31.6047
Evaluate side-chains
  139 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  517 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 75 optimal weight:    0.3980
   chunk 12 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.187823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.160406 restraints weight = 9016.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 2.04
r_work: 0.3723 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6788  Z= 0.143
  Angle     :  0.602   8.479   9189  Z= 0.316
  Chirality :  0.042   0.193    984
  Planarity :  0.004   0.046   1095
  Dihedral  : 11.202  59.997   1038
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.61 %
    Favored  : 78.58 %
  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:  0.56 (0.31), residues: 754
  helix:  1.41 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -2.59 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 514 
 HIS   0.002   0.001   HIS B 476 
 PHE   0.030   0.001   PHE B 394 
 TYR   0.027   0.002   TYR A 496 
 ARG   0.006   0.000   ARG B 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04303 (  424)
  hydrogen bonds       : angle       4.43581 ( 1263)
  covalent geometry    : bond        0.00325 ( 6787)
  covalent geometry    : angle       0.60207 ( 9189)
  Misc. bond           : bond        0.00079 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3153.24 seconds
wall clock time: 55 minutes 57.47 seconds (3357.47 seconds total)