Starting phenix.real_space_refine
on Thu Jul 24 19:26:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yfd_39220/07_2025/8yfd_39220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yfd_39220/07_2025/8yfd_39220.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yfd_39220/07_2025/8yfd_39220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yfd_39220/07_2025/8yfd_39220.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yfd_39220/07_2025/8yfd_39220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yfd_39220/07_2025/8yfd_39220.cif"
  }
  resolution = 3.57
  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=   0.082
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4414      2.51       5
     N    1054      2.21       5
     O    1088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3294
          Classifications: {'peptide': 396}
          Link IDs: {'PTRANS': 15, 'TRANS': 380}
    Chain: "B"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3294
          Classifications: {'peptide': 396}
          Link IDs: {'PTRANS': 15, 'TRANS': 380}
  Time building chain proxies: 4.76, per 1000 atoms: 0.72
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (79.2, 67.1, 125.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1088      8.00
     N    1054      7.00
     C    4414      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1504

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      73.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 258
      removed outlier: 3.619A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 4.856A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.629A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 360
      removed outlier: 3.948A  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 402
      removed outlier: 3.637A  pdb=" N   PHE A 394 " --> pdb=" O   GLY A 390 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.920A  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 476 through 501
      removed outlier: 4.326A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   GLU A 501 " --> pdb=" O   SER A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 3.559A  pdb=" N   ILE A 520 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE A 527 " --> pdb=" O   CYS A 523 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET A 532 " --> pdb=" O   TRP A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 571
      removed outlier: 4.026A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 583
      removed outlier: 3.713A  pdb=" N   GLN A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 622
      Proline residue:  A 598  - end of helix
      removed outlier: 4.225A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   PHE A 602 " --> pdb=" O   PRO A 598 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 258
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 3.673A  pdb=" N   ILE B 269 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 3.743A  pdb=" N   ILE B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.555A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 345
      No H-bonds generated for 'chain 'B' and resid 343 through 345'
    Processing helix  chain 'B' and resid 346 through 360
      removed outlier: 3.759A  pdb=" N   LEU B 359 " --> pdb=" O   MET B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 382
      removed outlier: 3.513A  pdb=" N   PHE B 379 " --> pdb=" O   LEU B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 399
    Processing helix  chain 'B' and resid 404 through 420
      removed outlier: 3.518A  pdb=" N   LEU B 410 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLU B 411 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   TYR B 412 " --> pdb=" O   MET B 408 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU B 420 " --> pdb=" O   PHE B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 473 through 501
      removed outlier: 4.112A  pdb=" N   GLY B 481 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.638A  pdb=" N   PHE B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   TYR B 512 " --> pdb=" O   MET B 508 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU B 513 " --> pdb=" O   VAL B 509 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   VAL B 516 " --> pdb=" O   TYR B 512 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER B 521 " --> pdb=" O   PHE B 517 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ILE B 527 " --> pdb=" O   CYS B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 571
      removed outlier: 4.180A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 580
    Processing helix  chain 'B' and resid 588 through 622
      removed outlier: 4.247A  pdb=" N   ILE B 592 " --> pdb=" O   SER B 588 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ALA B 593 " --> pdb=" O   GLY B 589 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 4.040A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE B 602 " --> pdb=" O   PRO B 598 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1230 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: 1.63

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1955
        1.35 -     1.46: 1935
        1.46 -     1.58: 2874
        1.58 -     1.70: 0
        1.70 -     1.82: 44
  Bond restraints: 6808
  Sorted by residual:
  bond pdb=" CA  THR A 261 "
       pdb=" CB  THR A 261 "
    ideal  model  delta    sigma   weight residual
    1.526  1.547 -0.021 1.53e-02 4.27e+03 1.88e+00
  bond pdb=" N   PRO A 475 "
       pdb=" CA  PRO A 475 "
    ideal  model  delta    sigma   weight residual
    1.474  1.465  0.009 7.40e-03 1.83e+04 1.40e+00
  bond pdb=" CA  HIS A 504 "
       pdb=" C   HIS A 504 "
    ideal  model  delta    sigma   weight residual
    1.532  1.522  0.011 9.60e-03 1.09e+04 1.21e+00
  bond pdb=" CA  ILE B 339 "
       pdb=" CB  ILE B 339 "
    ideal  model  delta    sigma   weight residual
    1.527  1.540 -0.013 1.31e-02 5.83e+03 1.04e+00
  bond pdb=" CA  TYR B 367 "
       pdb=" C   TYR B 367 "
    ideal  model  delta    sigma   weight residual
    1.532  1.523  0.010 9.60e-03 1.09e+04 1.01e+00
  ... (remaining 6803 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 9087
        2.12 -     4.25: 152
        4.25 -     6.37: 23
        6.37 -     8.50: 4
        8.50 -    10.62: 2
  Bond angle restraints: 9268
  Sorted by residual:
  angle pdb=" N   ASP A 262 "
        pdb=" CA  ASP A 262 "
        pdb=" C   ASP A 262 "
      ideal   model   delta    sigma   weight residual
     114.64  107.72    6.92 1.52e+00 4.33e-01 2.07e+01
  angle pdb=" C   THR B 383 "
        pdb=" N   ALA B 384 "
        pdb=" CA  ALA B 384 "
      ideal   model   delta    sigma   weight residual
     121.80  130.88   -9.08 2.44e+00 1.68e-01 1.39e+01
  angle pdb=" C   ARG B 308 "
        pdb=" N   SER B 309 "
        pdb=" CA  SER B 309 "
      ideal   model   delta    sigma   weight residual
     121.54  127.58   -6.04 1.91e+00 2.74e-01 9.99e+00
  angle pdb=" CA  TRP B 395 "
        pdb=" CB  TRP B 395 "
        pdb=" CG  TRP B 395 "
      ideal   model   delta    sigma   weight residual
     113.60  119.47   -5.87 1.90e+00 2.77e-01 9.53e+00
  angle pdb=" CA  TYR B 290 "
        pdb=" CB  TYR B 290 "
        pdb=" CG  TYR B 290 "
      ideal   model   delta    sigma   weight residual
     113.90  119.46   -5.56 1.80e+00 3.09e-01 9.53e+00
  ... (remaining 9263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 3194
       16.45 -    32.91: 458
       32.91 -    49.36: 179
       49.36 -    65.81: 34
       65.81 -    82.26: 3
  Dihedral angle restraints: 3868
    sinusoidal: 1532
      harmonic: 2336
  Sorted by residual:
  dihedral pdb=" CA  GLN B 399 "
           pdb=" C   GLN B 399 "
           pdb=" N   LEU B 400 "
           pdb=" CA  LEU B 400 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.83   24.17     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  ALA B 384 "
           pdb=" C   ALA B 384 "
           pdb=" N   PRO B 385 "
           pdb=" CA  PRO B 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.86  -21.14     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  ILE A 342 "
           pdb=" C   ILE A 342 "
           pdb=" N   PRO A 343 "
           pdb=" CA  PRO A 343 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.24  -19.76     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 3865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 653
       0.034 -    0.067: 264
       0.067 -    0.101: 75
       0.101 -    0.135: 17
       0.135 -    0.168: 3
  Chirality restraints: 1012
  Sorted by residual:
  chirality pdb=" CA  GLN B 399 "
            pdb=" N   GLN B 399 "
            pdb=" C   GLN B 399 "
            pdb=" CB  GLN B 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CG  LEU B 311 "
            pdb=" CB  LEU B 311 "
            pdb=" CD1 LEU B 311 "
            pdb=" CD2 LEU B 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CB  THR A 507 "
            pdb=" CA  THR A 507 "
            pdb=" OG1 THR A 507 "
            pdb=" CG2 THR A 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 4.88e-01
  ... (remaining 1009 not shown)

  Planarity restraints: 1134
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 395 "   -0.021 2.00e-02 2.50e+03   1.62e-02 6.59e+00
        pdb=" CG  TRP B 395 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 395 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 395 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 395 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 395 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 395 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 395 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 395 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 395 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 310 "   -0.010 2.00e-02 2.50e+03   1.95e-02 3.82e+00
        pdb=" C   ASN B 310 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASN B 310 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU B 311 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 384 "    0.031 5.00e-02 4.00e+02   4.69e-02 3.52e+00
        pdb=" N   PRO B 385 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 385 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 385 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1131 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 431
        2.74 -     3.28: 6891
        3.28 -     3.82: 10931
        3.82 -     4.36: 11858
        4.36 -     4.90: 20548
  Nonbonded interactions: 50659
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 579 "
            pdb=" OG1 THR A 583 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   SER A 578 "
            pdb=" OG1 THR A 582 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ARG B 308 "
            pdb=" OG  SER B 309 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   ARG A 466 "
            pdb=" OG1 THR A 470 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   ILE A 271 "
            pdb=" OH  TYR A 352 "
     model   vdw
     2.278 3.040
  ... (remaining 50654 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.740
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.930
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
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   0.032   6810  Z= 0.149
  Angle     :  0.678  10.623   9272  Z= 0.384
  Chirality :  0.040   0.168   1012
  Planarity :  0.004   0.047   1134
  Dihedral  : 17.761  82.263   2358
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.09 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 29.97 %
    Favored  : 69.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.32), residues: 788
  helix:  1.21 (0.22), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.80 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP B 395 
 HIS   0.004   0.001   HIS B 441 
 PHE   0.012   0.001   PHE A 394 
 TYR   0.015   0.001   TYR A 518 
 ARG   0.004   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12708 (  410)
  hydrogen bonds       : angle       5.45319 ( 1230)
  SS BOND              : bond        0.00084 (    2)
  SS BOND              : angle       1.46552 (    4)
  covalent geometry    : bond        0.00297 ( 6808)
  covalent geometry    : angle       0.67750 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 140
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A  489 MET cc_start: 0.7149 (tmm) cc_final: 0.6595 (tmm)
  outliers start: 4
  outliers final: 4
  residues processed: 142
  average time/residue: 0.1642
  time to fit residues: 31.8797
Evaluate side-chains
  129 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  398 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0370
   chunk 32 optimal weight:    0.0670
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 61 optimal weight:    0.0060
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.2812

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.178745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.144803 restraints weight = 9684.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.148483 restraints weight = 6075.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.150871 restraints weight = 4590.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.0846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6810  Z= 0.119
  Angle     :  0.565   9.015   9272  Z= 0.294
  Chirality :  0.039   0.147   1012
  Planarity :  0.005   0.064   1134
  Dihedral  :  5.732  59.155    879
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.22 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 25.43 %
    Favored  : 70.17 %
  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:  0.67 (0.31), residues: 788
  helix:  1.65 (0.22), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.87 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP B 395 
 HIS   0.005   0.001   HIS B 441 
 PHE   0.014   0.001   PHE A 394 
 TYR   0.012   0.001   TYR A 518 
 ARG   0.004   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04420 (  410)
  hydrogen bonds       : angle       3.88177 ( 1230)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       1.25620 (    4)
  covalent geometry    : bond        0.00239 ( 6808)
  covalent geometry    : angle       0.56431 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 138
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A  263 ARG cc_start: 0.5733 (tpt170) cc_final: 0.5308 (ttt90)
REVERT: A  497 SER cc_start: 0.8381 (m) cc_final: 0.8061 (p)
REVERT: A  518 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7355 (m-80)
REVERT: B  452 GLN cc_start: 0.7989 (tp40) cc_final: 0.7717 (tp40)
REVERT: B  508 MET cc_start: 0.7550 (mtm) cc_final: 0.7135 (mpp)
REVERT: B  613 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6803 (pp20)
  outliers start: 31
  outliers final: 14
  residues processed: 158
  average time/residue: 0.1584
  time to fit residues: 34.3678
Evaluate side-chains
  136 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  424 ASP
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  518 TYR
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  453 CYS
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  544 ASN
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 24 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0270
   chunk 66 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 441 HIS
B 479 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.176846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142757 restraints weight = 9794.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.146383 restraints weight = 6062.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.148713 restraints weight = 4554.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6810  Z= 0.119
  Angle     :  0.551   9.261   9272  Z= 0.283
  Chirality :  0.039   0.136   1012
  Planarity :  0.004   0.065   1134
  Dihedral  :  5.091  56.597    876
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.58 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 26.14 %
    Favored  : 68.32 %
  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:  0.89 (0.32), residues: 788
  helix:  1.83 (0.22), residues: 565
  sheet:  None (None), residues: 0
  loop : -2.87 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 395 
 HIS   0.004   0.001   HIS B 441 
 PHE   0.015   0.001   PHE A 394 
 TYR   0.015   0.001   TYR A 496 
 ARG   0.003   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04263 (  410)
  hydrogen bonds       : angle       3.66992 ( 1230)
  SS BOND              : bond        0.00213 (    2)
  SS BOND              : angle       1.49880 (    4)
  covalent geometry    : bond        0.00257 ( 6808)
  covalent geometry    : angle       0.55051 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.5603 (tpt170) cc_final: 0.5365 (ttt90)
REVERT: A  497 SER cc_start: 0.8311 (m) cc_final: 0.8026 (p)
REVERT: A  605 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7902 (t80)
REVERT: B  502 ARG cc_start: 0.7897 (tmm-80) cc_final: 0.7571 (ttm-80)
REVERT: B  613 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6294 (tm-30)
  outliers start: 39
  outliers final: 21
  residues processed: 163
  average time/residue: 0.1501
  time to fit residues: 33.7309
Evaluate side-chains
  144 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  605 PHE
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  544 ASN
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 24 optimal weight:    0.1980
   chunk 77 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    6.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 441 HIS
B 462 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.176690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.142463 restraints weight = 10042.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145993 restraints weight = 6222.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.148304 restraints weight = 4705.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6810  Z= 0.125
  Angle     :  0.560   9.331   9272  Z= 0.290
  Chirality :  0.040   0.199   1012
  Planarity :  0.004   0.062   1134
  Dihedral  :  4.677  54.446    874
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.35 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 25.99 %
    Favored  : 68.61 %
  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:  0.91 (0.32), residues: 788
  helix:  1.86 (0.22), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.92 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 395 
 HIS   0.005   0.001   HIS B 441 
 PHE   0.016   0.001   PHE A 394 
 TYR   0.011   0.001   TYR A 496 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04305 (  410)
  hydrogen bonds       : angle       3.72197 ( 1230)
  SS BOND              : bond        0.00411 (    2)
  SS BOND              : angle       1.34442 (    4)
  covalent geometry    : bond        0.00281 ( 6808)
  covalent geometry    : angle       0.55952 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 128
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6221 (m-80)
REVERT: A  497 SER cc_start: 0.8364 (m) cc_final: 0.8055 (p)
REVERT: B  502 ARG cc_start: 0.7921 (tmm-80) cc_final: 0.7651 (ttm-80)
REVERT: B  587 HIS cc_start: 0.6442 (OUTLIER) cc_final: 0.6157 (t-90)
REVERT: B  613 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6319 (tm-30)
  outliers start: 38
  outliers final: 27
  residues processed: 154
  average time/residue: 0.1588
  time to fit residues: 33.7021
Evaluate side-chains
  152 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 122
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  518 TYR
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  544 ASN
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0030
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0030
   overall best weight:    0.5000

-------------------------------------------------------------------------------
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 = 0.4061 r_free = 0.4061 target = 0.176880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.142323 restraints weight = 9949.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145968 restraints weight = 6264.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.148363 restraints weight = 4748.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6810  Z= 0.116
  Angle     :  0.539   9.365   9272  Z= 0.279
  Chirality :  0.040   0.164   1012
  Planarity :  0.004   0.059   1134
  Dihedral  :  4.559  51.075    874
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.58 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 25.71 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.32), residues: 788
  helix:  1.92 (0.22), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.93 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 395 
 HIS   0.005   0.001   HIS B 441 
 PHE   0.015   0.001   PHE A 394 
 TYR   0.011   0.001   TYR A 496 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  410)
  hydrogen bonds       : angle       3.63917 ( 1230)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       1.28236 (    4)
  covalent geometry    : bond        0.00255 ( 6808)
  covalent geometry    : angle       0.53827 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 130
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6196 (m-80)
REVERT: A  497 SER cc_start: 0.8343 (m) cc_final: 0.8055 (p)
REVERT: A  512 TYR cc_start: 0.7907 (m-10) cc_final: 0.7567 (m-80)
REVERT: B  335 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6920 (m-80)
REVERT: B  408 MET cc_start: 0.7491 (mmm) cc_final: 0.7268 (mmm)
REVERT: B  502 ARG cc_start: 0.7934 (tmm-80) cc_final: 0.7700 (tmm-80)
REVERT: B  508 MET cc_start: 0.7251 (mtm) cc_final: 0.6949 (mpp)
REVERT: B  587 HIS cc_start: 0.6173 (OUTLIER) cc_final: 0.5925 (t-90)
REVERT: B  613 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6305 (tm-30)
  outliers start: 39
  outliers final: 24
  residues processed: 157
  average time/residue: 0.1547
  time to fit residues: 33.7180
Evaluate side-chains
  152 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 TYR
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  518 TYR
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  544 ASN
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.174582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.140239 restraints weight = 9777.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.143823 restraints weight = 6159.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.146123 restraints weight = 4651.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6810  Z= 0.134
  Angle     :  0.560   9.392   9272  Z= 0.290
  Chirality :  0.040   0.154   1012
  Planarity :  0.004   0.056   1134
  Dihedral  :  4.505  48.750    874
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.71 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 27.27 %
    Favored  : 67.61 %
  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 (0.31), residues: 788
  helix:  1.88 (0.22), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.92 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 395 
 HIS   0.005   0.001   HIS B 441 
 PHE   0.016   0.001   PHE A 394 
 TYR   0.010   0.001   TYR A 496 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04428 (  410)
  hydrogen bonds       : angle       3.72493 ( 1230)
  SS BOND              : bond        0.00134 (    2)
  SS BOND              : angle       1.29450 (    4)
  covalent geometry    : bond        0.00308 ( 6808)
  covalent geometry    : angle       0.55972 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6281 (m-80)
REVERT: A  497 SER cc_start: 0.8384 (m) cc_final: 0.8131 (p)
REVERT: A  512 TYR cc_start: 0.7890 (m-10) cc_final: 0.7523 (m-80)
REVERT: A  518 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7303 (m-80)
REVERT: B  335 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6948 (m-80)
REVERT: B  502 ARG cc_start: 0.7975 (tmm-80) cc_final: 0.7763 (tmm-80)
REVERT: B  508 MET cc_start: 0.7038 (mtm) cc_final: 0.6804 (mpp)
REVERT: B  613 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6292 (tm-30)
  outliers start: 36
  outliers final: 26
  residues processed: 148
  average time/residue: 0.1504
  time to fit residues: 31.0083
Evaluate side-chains
  148 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  518 TYR
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  544 ASN
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0070
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.6598

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.174641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.139962 restraints weight = 9960.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.143619 restraints weight = 6286.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145920 restraints weight = 4775.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6810  Z= 0.127
  Angle     :  0.563   9.498   9272  Z= 0.292
  Chirality :  0.040   0.149   1012
  Planarity :  0.004   0.055   1134
  Dihedral  :  4.484  47.787    874
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.84 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 27.56 %
    Favored  : 67.33 %
  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:  0.90 (0.31), residues: 788
  helix:  1.87 (0.22), residues: 565
  sheet:  None (None), residues: 0
  loop : -2.97 (0.41), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 395 
 HIS   0.005   0.001   HIS B 441 
 PHE   0.015   0.001   PHE A 394 
 TYR   0.010   0.001   TYR A 496 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04384 (  410)
  hydrogen bonds       : angle       3.73154 ( 1230)
  SS BOND              : bond        0.00169 (    2)
  SS BOND              : angle       1.24630 (    4)
  covalent geometry    : bond        0.00289 ( 6808)
  covalent geometry    : angle       0.56248 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 125
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6308 (m-80)
REVERT: A  497 SER cc_start: 0.8381 (m) cc_final: 0.8132 (p)
REVERT: A  518 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7127 (m-80)
REVERT: B  335 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6936 (m-80)
REVERT: B  452 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8489 (tp40)
REVERT: B  508 MET cc_start: 0.6907 (mtm) cc_final: 0.6692 (mpp)
REVERT: B  613 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6309 (tm-30)
  outliers start: 36
  outliers final: 23
  residues processed: 148
  average time/residue: 0.1675
  time to fit residues: 34.8250
Evaluate side-chains
  153 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  518 TYR
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  544 ASN
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.173687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.139064 restraints weight = 9976.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.142621 restraints weight = 6271.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144942 restraints weight = 4741.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6810  Z= 0.134
  Angle     :  0.571   9.451   9272  Z= 0.296
  Chirality :  0.040   0.153   1012
  Planarity :  0.004   0.052   1134
  Dihedral  :  4.480  45.997    874
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.47 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 27.84 %
    Favored  : 67.19 %
  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:  0.87 (0.31), residues: 788
  helix:  1.83 (0.22), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.93 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 395 
 HIS   0.004   0.001   HIS B 441 
 PHE   0.016   0.001   PHE A 394 
 TYR   0.009   0.001   TYR A 496 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04502 (  410)
  hydrogen bonds       : angle       3.73687 ( 1230)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       1.60220 (    4)
  covalent geometry    : bond        0.00310 ( 6808)
  covalent geometry    : angle       0.56989 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6332 (m-80)
REVERT: A  497 SER cc_start: 0.8376 (m) cc_final: 0.8132 (p)
REVERT: A  518 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7436 (m-80)
REVERT: B  269 ILE cc_start: 0.6212 (OUTLIER) cc_final: 0.5809 (tp)
REVERT: B  283 PHE cc_start: 0.8021 (m-10) cc_final: 0.7761 (m-10)
REVERT: B  408 MET cc_start: 0.7840 (mmm) cc_final: 0.7558 (mmm)
REVERT: B  613 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6379 (tm-30)
  outliers start: 35
  outliers final: 25
  residues processed: 149
  average time/residue: 0.1545
  time to fit residues: 32.1388
Evaluate side-chains
  149 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  518 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  453 CYS
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  544 ASN
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0050
   chunk 0 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0570
   chunk 57 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6116

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.175001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.140864 restraints weight = 9843.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.144399 restraints weight = 6104.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.146421 restraints weight = 4602.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6810  Z= 0.125
  Angle     :  0.571   9.565   9272  Z= 0.294
  Chirality :  0.040   0.148   1012
  Planarity :  0.004   0.051   1134
  Dihedral  :  4.451  44.971    874
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.22 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 27.70 %
    Favored  : 67.47 %
  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 (0.31), residues: 788
  helix:  1.90 (0.22), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.96 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 395 
 HIS   0.005   0.001   HIS B 441 
 PHE   0.014   0.001   PHE A 394 
 TYR   0.009   0.001   TYR A 496 
 ARG   0.002   0.000   ARG B 502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  410)
  hydrogen bonds       : angle       3.69388 ( 1230)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       1.53469 (    4)
  covalent geometry    : bond        0.00280 ( 6808)
  covalent geometry    : angle       0.57035 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6307 (m-80)
REVERT: A  497 SER cc_start: 0.8325 (m) cc_final: 0.8093 (p)
REVERT: B  283 PHE cc_start: 0.7997 (m-10) cc_final: 0.7724 (m-10)
REVERT: B  613 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6365 (tm-30)
  outliers start: 34
  outliers final: 25
  residues processed: 146
  average time/residue: 0.1869
  time to fit residues: 38.3707
Evaluate side-chains
  148 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  518 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  453 CYS
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  544 ASN
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 71 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.174258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.139675 restraints weight = 9949.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.143226 restraints weight = 6226.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.145558 restraints weight = 4719.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6810  Z= 0.134
  Angle     :  0.583   9.562   9272  Z= 0.299
  Chirality :  0.040   0.151   1012
  Planarity :  0.004   0.049   1134
  Dihedral  :  4.448  43.625    874
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.47 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 28.69 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.31), residues: 788
  helix:  1.87 (0.22), residues: 567
  sheet:  None (None), residues: 0
  loop : -2.96 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 395 
 HIS   0.005   0.001   HIS B 441 
 PHE   0.015   0.001   PHE A 394 
 TYR   0.009   0.001   TYR A 496 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04505 (  410)
  hydrogen bonds       : angle       3.73326 ( 1230)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       1.60737 (    4)
  covalent geometry    : bond        0.00306 ( 6808)
  covalent geometry    : angle       0.58215 ( 9268)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6259 (m-80)
REVERT: A  497 SER cc_start: 0.8335 (m) cc_final: 0.8104 (p)
REVERT: B  283 PHE cc_start: 0.8018 (m-10) cc_final: 0.7784 (m-10)
REVERT: B  408 MET cc_start: 0.7668 (mmm) cc_final: 0.7408 (mmm)
REVERT: B  613 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6385 (tm-30)
  outliers start: 30
  outliers final: 26
  residues processed: 144
  average time/residue: 0.2074
  time to fit residues: 42.9010
Evaluate side-chains
  147 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  299 HIS
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  487 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  518 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  453 CYS
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  544 ASN
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0370
   chunk 4 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 74 optimal weight:    0.3980
   chunk 64 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.6058

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.175322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.140758 restraints weight = 9950.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.144436 restraints weight = 6201.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.146745 restraints weight = 4669.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6810  Z= 0.127
  Angle     :  0.581   9.613   9272  Z= 0.296
  Chirality :  0.040   0.150   1012
  Planarity :  0.004   0.049   1134
  Dihedral  :  4.439  42.620    874
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.47 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 28.84 %
    Favored  : 67.33 %
  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:  0.98 (0.31), residues: 788
  helix:  1.93 (0.22), residues: 567
  sheet:  None (None), residues: 0
  loop : -2.97 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 395 
 HIS   0.005   0.001   HIS B 441 
 PHE   0.013   0.001   PHE A 394 
 TYR   0.009   0.001   TYR A 496 
 ARG   0.002   0.000   ARG B 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  410)
  hydrogen bonds       : angle       3.70151 ( 1230)
  SS BOND              : bond        0.00152 (    2)
  SS BOND              : angle       1.57615 (    4)
  covalent geometry    : bond        0.00285 ( 6808)
  covalent geometry    : angle       0.57979 ( 9268)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2433.64 seconds
wall clock time: 43 minutes 27.32 seconds (2607.32 seconds total)