Starting phenix.real_space_refine
on Sat Apr 26 21:32:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jys_36730/04_2025/8jys_36730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jys_36730/04_2025/8jys_36730.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jys_36730/04_2025/8jys_36730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jys_36730/04_2025/8jys_36730.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jys_36730/04_2025/8jys_36730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jys_36730/04_2025/8jys_36730.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.042
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      16      5.16       5
     C    2271      2.51       5
     N     587      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3522
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 241
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1514
          Classifications: {'peptide': 189}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 176}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 253
          Classifications: {'peptide': 32}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1514
          Classifications: {'peptide': 189}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 176}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.01, per 1000 atoms: 0.85
  Number of scatterers: 3522
  At special positions: 0
  Unit cell: (90.094, 67.36, 119.564, 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      16     16.00
     O     648      8.00
     N     587      7.00
     C    2271      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 391 " - pdb=" SG  CYS D 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 480 " - pdb=" SG  CYS D 488 " 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: 0.90
  Conformation dependent library (CDL) restraints added in 439.3 milliseconds
  

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  822

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 5 sheets defined
      11.8% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 4.391A  pdb=" N   LEU B 390 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
      removed outlier: 4.104A  pdb=" N   ILE B 410 " --> pdb=" O   GLU B 406 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ALA B 411 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 406 through 411'
    Processing helix  chain 'D' and resid 338 through 343
    Processing helix  chain 'D' and resid 365 through 370
    Processing helix  chain 'D' and resid 383 through 388
    Processing helix  chain 'D' and resid 404 through 410
      removed outlier: 3.808A  pdb=" N   VAL D 407 " --> pdb=" O   GLY D 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.709A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE B 402 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.709A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AA4, first strand: chain 'D' and resid 356 through 358
      removed outlier: 4.195A  pdb=" N   VAL D 395 " --> pdb=" O   ILE D 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 473 through 474
      removed outlier: 3.969A  pdb=" N   TYR D 489 " --> pdb=" O   TYR D 473 " (cutoff:3.500A)

    56 hydrogen bonds defined for protein.
    129 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: 0.70

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1112
        1.34 -     1.47: 1024
        1.47 -     1.59: 1473
        1.59 -     1.72: 0
        1.72 -     1.84: 16
  Bond restraints: 3625
  Sorted by residual:
  bond pdb=" N   LEU C 109 "
       pdb=" CA  LEU C 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.49e-02 4.50e+03 5.38e+00
  bond pdb=" C   GLU A  57 "
       pdb=" N   PRO A  58 "
    ideal  model  delta    sigma   weight residual
    1.328  1.353 -0.025 1.26e-02 6.30e+03 3.84e+00
  bond pdb=" C   ALA D 520 "
       pdb=" N   PRO D 521 "
    ideal  model  delta    sigma   weight residual
    1.332  1.355 -0.023 1.33e-02 5.65e+03 3.07e+00
  bond pdb=" C   PRO B 373 "
       pdb=" O   PRO B 373 "
    ideal  model  delta    sigma   weight residual
    1.235  1.218  0.017 1.30e-02 5.92e+03 1.81e+00
  bond pdb=" C   PRO D 521 "
       pdb=" O   PRO D 521 "
    ideal  model  delta    sigma   weight residual
    1.233  1.218  0.015 1.23e-02 6.61e+03 1.46e+00
  ... (remaining 3620 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 4704
        2.01 -     4.03: 179
        4.03 -     6.04: 33
        6.04 -     8.06: 11
        8.06 -    10.07: 3
  Bond angle restraints: 4930
  Sorted by residual:
  angle pdb=" C   ASN D 422 "
        pdb=" N   TYR D 423 "
        pdb=" CA  TYR D 423 "
      ideal   model   delta    sigma   weight residual
     121.54  131.56  -10.02 1.91e+00 2.74e-01 2.75e+01
  angle pdb=" CA  TYR D 423 "
        pdb=" CB  TYR D 423 "
        pdb=" CG  TYR D 423 "
      ideal   model   delta    sigma   weight residual
     113.90  120.74   -6.84 1.80e+00 3.09e-01 1.44e+01
  angle pdb=" N   SER B 366 "
        pdb=" CA  SER B 366 "
        pdb=" C   SER B 366 "
      ideal   model   delta    sigma   weight residual
     113.43  108.71    4.72 1.26e+00 6.30e-01 1.40e+01
  angle pdb=" CB  LYS B 356 "
        pdb=" CG  LYS B 356 "
        pdb=" CD  LYS B 356 "
      ideal   model   delta    sigma   weight residual
     111.30  119.15   -7.85 2.30e+00 1.89e-01 1.16e+01
  angle pdb=" C   GLU B 465 "
        pdb=" CA  GLU B 465 "
        pdb=" CB  GLU B 465 "
      ideal   model   delta    sigma   weight residual
     113.37  108.12    5.25 1.61e+00 3.86e-01 1.06e+01
  ... (remaining 4925 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 1704
       16.01 -    32.01: 307
       32.01 -    48.02: 81
       48.02 -    64.02: 20
       64.02 -    80.02: 6
  Dihedral angle restraints: 2118
    sinusoidal: 826
      harmonic: 1292
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -21.65  -64.35     1      1.00e+01 1.00e-02 5.44e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.59   46.41     1      1.00e+01 1.00e-02 2.98e+01
  dihedral pdb=" CB  CYS D 379 "
           pdb=" SG  CYS D 379 "
           pdb=" SG  CYS D 432 "
           pdb=" CB  CYS D 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.27   40.73     1      1.00e+01 1.00e-02 2.33e+01
  ... (remaining 2115 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 272
       0.031 -    0.061: 132
       0.061 -    0.092: 71
       0.092 -    0.123: 30
       0.123 -    0.153: 4
  Chirality restraints: 509
  Sorted by residual:
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  VAL D 511 "
            pdb=" N   VAL D 511 "
            pdb=" C   VAL D 511 "
            pdb=" CB  VAL D 511 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.68e-01
  chirality pdb=" CA  ILE B 402 "
            pdb=" N   ILE B 402 "
            pdb=" C   ILE B 402 "
            pdb=" CB  ILE B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.58e-01
  ... (remaining 506 not shown)

  Planarity restraints: 644
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 372 "    0.053 5.00e-02 4.00e+02   7.93e-02 1.01e+01
        pdb=" N   PRO D 373 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO D 373 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO D 373 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  57 "    0.043 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO C  58 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO C  58 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  58 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 509 "   -0.184 9.50e-02 1.11e+02   8.27e-02 4.24e+00
        pdb=" NE  ARG D 509 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 509 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 509 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 641 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 349
        2.74 -     3.28: 3830
        3.28 -     3.82: 5469
        3.82 -     4.36: 6023
        4.36 -     4.90: 9633
  Nonbonded interactions: 25304
  Sorted by model distance:
  nonbonded pdb=" O   PHE D 347 "
            pdb=" OH  TYR D 451 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG  SER D 383 "
            pdb=" NZ  LYS D 386 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OG  SER D 438 "
            pdb=" OD1 ASP D 442 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" NZ  LYS D 478 "
            pdb=" O   PRO D 479 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.245 3.040
  ... (remaining 25299 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 49 through 116)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             0.360
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.570
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3633  Z= 0.199
  Angle     :  0.969  10.071   4946  Z= 0.518
  Chirality :  0.048   0.153    509
  Planarity :  0.008   0.083    644
  Dihedral  : 17.514  80.024   1272
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 20.35
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 12.71 %
    Favored  : 86.12 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 38.34 %
    Favored  : 59.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.38), residues: 425
  helix: -2.42 (0.72), residues: 44
  sheet: -0.81 (0.64), residues: 68
  loop : -2.90 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B 436 
 HIS   0.001   0.000   HIS B 505 
 PHE   0.029   0.002   PHE B 456 
 TYR   0.022   0.002   TYR B 508 
 ARG   0.012   0.001   ARG B 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20907 (   53)
  hydrogen bonds       : angle       7.89847 (  129)
  SS BOND              : bond        0.00352 (    8)
  SS BOND              : angle       2.06712 (   16)
  covalent geometry    : bond        0.00412 ( 3625)
  covalent geometry    : angle       0.96358 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  374 PHE cc_start: 0.7908 (t80) cc_final: 0.7666 (m-80)
REVERT: B  451 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80)
REVERT: D  516 GLU cc_start: 0.7900 (tp30) cc_final: 0.7482 (tm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 105
  average time/residue: 0.2088
  time to fit residues: 25.5403
Evaluate side-chains
  102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 31 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
D 422 ASN
D 474 GLN
D 481 ASN
D 487 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.118320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.098965 restraints weight = 12806.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.102018 restraints weight = 7888.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.104279 restraints weight = 5474.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3633  Z= 0.156
  Angle     :  0.769  12.048   4946  Z= 0.387
  Chirality :  0.046   0.159    509
  Planarity :  0.006   0.052    644
  Dihedral  :  5.630  20.140    492
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 11.29 %
    Favored  : 87.53 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  5.36 %
    Favored  : 94.10 %
  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: -3.22 (0.38), residues: 425
  helix: -3.54 (0.49), residues: 46
  sheet: -0.45 (0.63), residues: 64
  loop : -2.49 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 436 
 HIS   0.007   0.002   HIS B 505 
 PHE   0.023   0.002   PHE D 375 
 TYR   0.023   0.002   TYR B 423 
 ARG   0.009   0.001   ARG D 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (   53)
  hydrogen bonds       : angle       6.81718 (  129)
  SS BOND              : bond        0.00516 (    8)
  SS BOND              : angle       1.96758 (   16)
  covalent geometry    : bond        0.00344 ( 3625)
  covalent geometry    : angle       0.76172 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 ARG cc_start: 0.7553 (mtt180) cc_final: 0.7288 (mtt90)
REVERT: B  495 TYR cc_start: 0.6467 (m-10) cc_final: 0.6245 (m-80)
REVERT: D  335 LEU cc_start: 0.8971 (mm) cc_final: 0.8678 (tp)
REVERT: D  396 TYR cc_start: 0.8494 (m-80) cc_final: 0.8272 (m-80)
REVERT: D  402 ILE cc_start: 0.9027 (tp) cc_final: 0.8746 (tp)
REVERT: D  472 ILE cc_start: 0.8593 (tp) cc_final: 0.8297 (tp)
REVERT: D  473 TYR cc_start: 0.8906 (t80) cc_final: 0.8416 (t80)
REVERT: D  516 GLU cc_start: 0.8509 (tp30) cc_final: 0.7567 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1931
  time to fit residues: 28.3683
Evaluate side-chains
  103 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 32 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.1980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.117620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.098278 restraints weight = 12768.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.101316 restraints weight = 7809.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.103540 restraints weight = 5395.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3633  Z= 0.129
  Angle     :  0.702  10.911   4946  Z= 0.353
  Chirality :  0.046   0.179    509
  Planarity :  0.005   0.044    644
  Dihedral  :  5.454  19.273    492
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 11.76 %
    Favored  : 87.29 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.68 %
    Favored  : 97.05 %
  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: -3.15 (0.38), residues: 425
  helix: -3.05 (0.56), residues: 52
  sheet: -0.50 (0.60), residues: 69
  loop : -2.49 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 436 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.016   0.002   PHE D 400 
 TYR   0.020   0.001   TYR D 501 
 ARG   0.006   0.001   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03469 (   53)
  hydrogen bonds       : angle       6.61733 (  129)
  SS BOND              : bond        0.00213 (    8)
  SS BOND              : angle       1.29144 (   16)
  covalent geometry    : bond        0.00285 ( 3625)
  covalent geometry    : angle       0.69950 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASP cc_start: 0.7316 (p0) cc_final: 0.6847 (m-30)
REVERT: B  388 ASN cc_start: 0.7018 (t0) cc_final: 0.6575 (m-40)
REVERT: B  403 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7018 (mtt90)
REVERT: B  471 GLU cc_start: 0.9089 (tp30) cc_final: 0.8826 (tp30)
REVERT: B  495 TYR cc_start: 0.6486 (m-10) cc_final: 0.6220 (m-80)
REVERT: D  335 LEU cc_start: 0.8939 (mm) cc_final: 0.8660 (tp)
REVERT: D  394 ASN cc_start: 0.9222 (t0) cc_final: 0.8368 (p0)
REVERT: D  402 ILE cc_start: 0.9098 (tp) cc_final: 0.8857 (tp)
REVERT: D  425 LEU cc_start: 0.9049 (pp) cc_final: 0.8837 (pp)
REVERT: D  462 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8839 (mtmm)
REVERT: D  473 TYR cc_start: 0.8868 (t80) cc_final: 0.8556 (t80)
REVERT: D  516 GLU cc_start: 0.8395 (tp30) cc_final: 0.7570 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2000
  time to fit residues: 31.9033
Evaluate side-chains
  105 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.113888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.093896 restraints weight = 13235.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.096897 restraints weight = 8225.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.099036 restraints weight = 5746.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3633  Z= 0.148
  Angle     :  0.707  10.596   4946  Z= 0.361
  Chirality :  0.046   0.172    509
  Planarity :  0.005   0.045    644
  Dihedral  :  5.487  18.522    492
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 11.76 %
    Favored  : 87.29 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  3.22 %
    Favored  : 96.51 %
  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: -3.15 (0.38), residues: 425
  helix: -2.85 (0.57), residues: 52
  sheet: -0.57 (0.60), residues: 68
  loop : -2.51 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  53 
 HIS   0.002   0.000   HIS B 519 
 PHE   0.016   0.002   PHE B 456 
 TYR   0.019   0.002   TYR B 423 
 ARG   0.006   0.001   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03535 (   53)
  hydrogen bonds       : angle       6.62385 (  129)
  SS BOND              : bond        0.00331 (    8)
  SS BOND              : angle       1.56479 (   16)
  covalent geometry    : bond        0.00335 ( 3625)
  covalent geometry    : angle       0.70237 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.9413 (tppt) cc_final: 0.9206 (tppt)
REVERT: B  388 ASN cc_start: 0.6907 (t0) cc_final: 0.6487 (m110)
REVERT: B  403 ARG cc_start: 0.7855 (mtt180) cc_final: 0.6755 (mtm-85)
REVERT: B  453 TYR cc_start: 0.8388 (t80) cc_final: 0.7928 (t80)
REVERT: B  471 GLU cc_start: 0.9113 (tp30) cc_final: 0.8912 (tp30)
REVERT: B  495 TYR cc_start: 0.6776 (m-10) cc_final: 0.5643 (m-80)
REVERT: D  340 GLU cc_start: 0.9119 (mp0) cc_final: 0.8879 (mp0)
REVERT: D  386 LYS cc_start: 0.8609 (pttt) cc_final: 0.8357 (pttp)
REVERT: D  394 ASN cc_start: 0.9319 (t0) cc_final: 0.8293 (p0)
REVERT: D  402 ILE cc_start: 0.9125 (tp) cc_final: 0.8824 (tp)
REVERT: D  406 GLU cc_start: 0.9052 (pm20) cc_final: 0.8696 (pm20)
REVERT: D  409 GLN cc_start: 0.8831 (mt0) cc_final: 0.8493 (tt0)
REVERT: D  424 LYS cc_start: 0.9096 (pptt) cc_final: 0.8750 (pptt)
REVERT: D  425 LEU cc_start: 0.9152 (pp) cc_final: 0.8727 (pp)
REVERT: D  473 TYR cc_start: 0.8827 (t80) cc_final: 0.8421 (t80)
REVERT: D  486 PHE cc_start: 0.7462 (t80) cc_final: 0.7106 (t80)
REVERT: D  516 GLU cc_start: 0.8418 (tp30) cc_final: 0.7400 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 130
  average time/residue: 0.1979
  time to fit residues: 29.9902
Evaluate side-chains
  99 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 22 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
B 481 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.106696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.087411 restraints weight = 13524.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.090236 restraints weight = 8483.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.092266 restraints weight = 5984.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.5025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3633  Z= 0.240
  Angle     :  0.804  12.041   4946  Z= 0.416
  Chirality :  0.050   0.177    509
  Planarity :  0.006   0.048    644
  Dihedral  :  6.207  21.014    492
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 17.42
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 13.65 %
    Favored  : 85.41 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  4.56 %
    Favored  : 94.91 %
  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: -3.43 (0.38), residues: 425
  helix: -2.66 (0.61), residues: 53
  sheet: -1.03 (0.57), residues: 69
  loop : -2.72 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 436 
 HIS   0.003   0.001   HIS B 519 
 PHE   0.039   0.003   PHE B 375 
 TYR   0.033   0.002   TYR B 453 
 ARG   0.007   0.001   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03881 (   53)
  hydrogen bonds       : angle       7.20761 (  129)
  SS BOND              : bond        0.00461 (    8)
  SS BOND              : angle       1.92823 (   16)
  covalent geometry    : bond        0.00534 ( 3625)
  covalent geometry    : angle       0.79777 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8385 (pm20) cc_final: 0.7221 (tp30)
REVERT: B  356 LYS cc_start: 0.9448 (tppt) cc_final: 0.9161 (tppt)
REVERT: B  409 GLN cc_start: 0.9091 (mp10) cc_final: 0.8744 (mt0)
REVERT: B  423 TYR cc_start: 0.8921 (t80) cc_final: 0.8566 (t80)
REVERT: B  453 TYR cc_start: 0.8829 (t80) cc_final: 0.8314 (t80)
REVERT: B  489 TYR cc_start: 0.7765 (m-80) cc_final: 0.7450 (m-80)
REVERT: D  335 LEU cc_start: 0.9143 (mm) cc_final: 0.8921 (tp)
REVERT: D  340 GLU cc_start: 0.9095 (mp0) cc_final: 0.8866 (mp0)
REVERT: D  396 TYR cc_start: 0.8728 (m-80) cc_final: 0.8333 (m-80)
REVERT: D  402 ILE cc_start: 0.9189 (tp) cc_final: 0.8894 (tp)
REVERT: D  406 GLU cc_start: 0.8931 (pm20) cc_final: 0.8616 (pm20)
REVERT: D  473 TYR cc_start: 0.9006 (t80) cc_final: 0.8684 (t80)
REVERT: D  506 GLN cc_start: 0.8611 (mt0) cc_final: 0.8366 (mt0)
  outliers start: 2
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1968
  time to fit residues: 26.5116
Evaluate side-chains
  89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 14 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
D 474 GLN
D 487 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.108435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.089324 restraints weight = 13733.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.092200 restraints weight = 8510.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.094271 restraints weight = 5938.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.5364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3633  Z= 0.166
  Angle     :  0.740  11.729   4946  Z= 0.376
  Chirality :  0.047   0.195    509
  Planarity :  0.005   0.056    644
  Dihedral  :  5.923  20.820    492
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 13.18 %
    Favored  : 85.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  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: -3.45 (0.38), residues: 425
  helix: -3.20 (0.58), residues: 49
  sheet: -1.06 (0.56), residues: 73
  loop : -2.65 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 436 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.030   0.002   PHE B 375 
 TYR   0.022   0.002   TYR B 453 
 ARG   0.005   0.001   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03373 (   53)
  hydrogen bonds       : angle       6.90609 (  129)
  SS BOND              : bond        0.00537 (    8)
  SS BOND              : angle       1.46911 (   16)
  covalent geometry    : bond        0.00377 ( 3625)
  covalent geometry    : angle       0.73628 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8456 (pm20) cc_final: 0.7343 (tp30)
REVERT: B  354 ASN cc_start: 0.9384 (t0) cc_final: 0.9130 (t0)
REVERT: B  356 LYS cc_start: 0.9422 (tppt) cc_final: 0.9140 (tppt)
REVERT: B  403 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7573 (mpp80)
REVERT: B  409 GLN cc_start: 0.9167 (mp10) cc_final: 0.8834 (mt0)
REVERT: B  489 TYR cc_start: 0.7762 (m-80) cc_final: 0.7559 (m-80)
REVERT: D  340 GLU cc_start: 0.9151 (mp0) cc_final: 0.8890 (mp0)
REVERT: D  394 ASN cc_start: 0.9333 (t0) cc_final: 0.8038 (p0)
REVERT: D  396 TYR cc_start: 0.8763 (m-80) cc_final: 0.8191 (m-80)
REVERT: D  402 ILE cc_start: 0.9077 (tp) cc_final: 0.8716 (tp)
REVERT: D  406 GLU cc_start: 0.9012 (pm20) cc_final: 0.8507 (pm20)
REVERT: D  472 ILE cc_start: 0.7688 (tp) cc_final: 0.7427 (tp)
REVERT: D  473 TYR cc_start: 0.8870 (t80) cc_final: 0.8662 (t80)
REVERT: D  516 GLU cc_start: 0.8426 (tp30) cc_final: 0.7407 (tm-30)
REVERT: D  518 LEU cc_start: 0.8966 (tp) cc_final: 0.8731 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1980
  time to fit residues: 27.5273
Evaluate side-chains
  97 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 31 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
D 474 GLN
D 487 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.108294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.089904 restraints weight = 13901.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.092653 restraints weight = 8678.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.094654 restraints weight = 6092.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.5549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3633  Z= 0.160
  Angle     :  0.737  11.632   4946  Z= 0.375
  Chirality :  0.047   0.193    509
  Planarity :  0.005   0.061    644
  Dihedral  :  5.848  21.433    492
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 15.29 %
    Favored  : 83.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  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: -3.48 (0.38), residues: 425
  helix: -3.39 (0.57), residues: 49
  sheet: -1.01 (0.58), residues: 69
  loop : -2.64 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 436 
 HIS   0.003   0.001   HIS B 519 
 PHE   0.020   0.002   PHE D 400 
 TYR   0.019   0.002   TYR B 453 
 ARG   0.005   0.001   ARG A 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (   53)
  hydrogen bonds       : angle       7.17446 (  129)
  SS BOND              : bond        0.00282 (    8)
  SS BOND              : angle       1.83755 (   16)
  covalent geometry    : bond        0.00361 ( 3625)
  covalent geometry    : angle       0.73079 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8471 (pm20) cc_final: 0.7392 (tp30)
REVERT: B  354 ASN cc_start: 0.9366 (t0) cc_final: 0.9113 (t0)
REVERT: B  356 LYS cc_start: 0.9417 (tppt) cc_final: 0.9102 (tppt)
REVERT: B  403 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7707 (mpp80)
REVERT: B  406 GLU cc_start: 0.8489 (mp0) cc_final: 0.8274 (mp0)
REVERT: B  409 GLN cc_start: 0.9113 (mp10) cc_final: 0.8726 (mt0)
REVERT: B  423 TYR cc_start: 0.8671 (t80) cc_final: 0.8312 (t80)
REVERT: D  340 GLU cc_start: 0.9130 (mp0) cc_final: 0.8861 (mp0)
REVERT: D  394 ASN cc_start: 0.9269 (t0) cc_final: 0.7956 (p0)
REVERT: D  396 TYR cc_start: 0.8638 (m-80) cc_final: 0.8039 (m-80)
REVERT: D  402 ILE cc_start: 0.9093 (tp) cc_final: 0.8800 (tp)
REVERT: D  406 GLU cc_start: 0.9015 (pm20) cc_final: 0.8505 (pm20)
REVERT: D  409 GLN cc_start: 0.8882 (mt0) cc_final: 0.8556 (tt0)
REVERT: D  473 TYR cc_start: 0.8865 (t80) cc_final: 0.8610 (t80)
REVERT: D  509 ARG cc_start: 0.8309 (ttm110) cc_final: 0.7934 (ttm170)
REVERT: D  516 GLU cc_start: 0.8374 (tp30) cc_final: 0.7342 (tm-30)
REVERT: D  518 LEU cc_start: 0.8996 (tp) cc_final: 0.8772 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2052
  time to fit residues: 27.2591
Evaluate side-chains
  97 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
D 474 GLN
D 487 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.106554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.088295 restraints weight = 13675.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.091070 restraints weight = 8438.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.093070 restraints weight = 5882.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.5845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3633  Z= 0.182
  Angle     :  0.764  11.536   4946  Z= 0.392
  Chirality :  0.049   0.213    509
  Planarity :  0.005   0.053    644
  Dihedral  :  6.081  24.296    492
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 15.53 %
    Favored  : 83.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  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: -3.44 (0.39), residues: 425
  helix: -3.49 (0.57), residues: 43
  sheet: -0.99 (0.60), residues: 68
  loop : -2.62 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 436 
 HIS   0.002   0.001   HIS D 519 
 PHE   0.036   0.002   PHE B 375 
 TYR   0.021   0.002   TYR B 453 
 ARG   0.006   0.001   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (   53)
  hydrogen bonds       : angle       7.18077 (  129)
  SS BOND              : bond        0.00323 (    8)
  SS BOND              : angle       1.97425 (   16)
  covalent geometry    : bond        0.00409 ( 3625)
  covalent geometry    : angle       0.75675 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8589 (pm20) cc_final: 0.7513 (tp30)
REVERT: B  354 ASN cc_start: 0.9366 (t0) cc_final: 0.9009 (t0)
REVERT: B  356 LYS cc_start: 0.9423 (tppt) cc_final: 0.9013 (tppt)
REVERT: B  403 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7640 (mpp80)
REVERT: B  406 GLU cc_start: 0.8506 (mp0) cc_final: 0.8268 (mp0)
REVERT: B  489 TYR cc_start: 0.7839 (m-80) cc_final: 0.7630 (m-80)
REVERT: D  340 GLU cc_start: 0.9138 (mp0) cc_final: 0.8877 (mp0)
REVERT: D  396 TYR cc_start: 0.8641 (m-80) cc_final: 0.8296 (m-80)
REVERT: D  402 ILE cc_start: 0.9013 (tp) cc_final: 0.8701 (tp)
REVERT: D  406 GLU cc_start: 0.8949 (pm20) cc_final: 0.8441 (pm20)
REVERT: D  409 GLN cc_start: 0.8939 (mt0) cc_final: 0.8583 (tt0)
REVERT: D  473 TYR cc_start: 0.8814 (t80) cc_final: 0.8528 (t80)
REVERT: D  509 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7776 (ttt180)
REVERT: D  516 GLU cc_start: 0.8332 (tp30) cc_final: 0.7895 (tm-30)
REVERT: D  518 LEU cc_start: 0.8979 (tp) cc_final: 0.8759 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2073
  time to fit residues: 27.7147
Evaluate side-chains
  93 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 39 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0040
   chunk 5 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0770
   overall best weight:    1.5154

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
D 474 GLN
D 487 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.110325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.092041 restraints weight = 13408.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.094809 restraints weight = 8324.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.096787 restraints weight = 5826.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.5923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3633  Z= 0.132
  Angle     :  0.723   8.501   4946  Z= 0.370
  Chirality :  0.047   0.204    509
  Planarity :  0.005   0.050    644
  Dihedral  :  5.788  23.001    492
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 13.88 %
    Favored  : 84.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  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: -3.34 (0.39), residues: 425
  helix: -3.18 (0.64), residues: 41
  sheet: -1.05 (0.57), residues: 73
  loop : -2.57 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 436 
 HIS   0.001   0.001   HIS B 519 
 PHE   0.019   0.002   PHE D 400 
 TYR   0.015   0.002   TYR D 421 
 ARG   0.006   0.001   ARG A 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (   53)
  hydrogen bonds       : angle       7.01184 (  129)
  SS BOND              : bond        0.00282 (    8)
  SS BOND              : angle       2.10120 (   16)
  covalent geometry    : bond        0.00296 ( 3625)
  covalent geometry    : angle       0.71421 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8503 (pm20) cc_final: 0.7382 (tp30)
REVERT: B  354 ASN cc_start: 0.9337 (t0) cc_final: 0.8949 (t0)
REVERT: B  356 LYS cc_start: 0.9399 (tppt) cc_final: 0.8963 (tppt)
REVERT: B  403 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7463 (mpp80)
REVERT: D  340 GLU cc_start: 0.9132 (mp0) cc_final: 0.8848 (mp0)
REVERT: D  358 ILE cc_start: 0.9009 (mp) cc_final: 0.8770 (mp)
REVERT: D  394 ASN cc_start: 0.9200 (t0) cc_final: 0.8249 (p0)
REVERT: D  396 TYR cc_start: 0.8508 (m-80) cc_final: 0.7908 (m-80)
REVERT: D  402 ILE cc_start: 0.9023 (tp) cc_final: 0.8705 (tp)
REVERT: D  406 GLU cc_start: 0.8988 (pm20) cc_final: 0.8483 (pm20)
REVERT: D  409 GLN cc_start: 0.8935 (mt0) cc_final: 0.8614 (tt0)
REVERT: D  473 TYR cc_start: 0.8597 (t80) cc_final: 0.8293 (t80)
REVERT: D  506 GLN cc_start: 0.8493 (mt0) cc_final: 0.7976 (mp10)
REVERT: D  509 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7904 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2071
  time to fit residues: 28.1895
Evaluate side-chains
  96 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    0.0570
   chunk 14 optimal weight:    0.5980
   chunk 9 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0870
   chunk 33 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 37 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
D 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.112892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.093745 restraints weight = 13414.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.096671 restraints weight = 8397.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.098714 restraints weight = 5921.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.6190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3633  Z= 0.132
  Angle     :  0.742  12.033   4946  Z= 0.378
  Chirality :  0.047   0.186    509
  Planarity :  0.005   0.054    644
  Dihedral  :  5.723  22.869    492
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 13.41 %
    Favored  : 85.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  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: -3.33 (0.38), residues: 425
  helix: -3.21 (0.63), residues: 43
  sheet: -1.04 (0.58), residues: 73
  loop : -2.56 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 436 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.041   0.002   PHE D 429 
 TYR   0.016   0.001   TYR D 421 
 ARG   0.007   0.001   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03383 (   53)
  hydrogen bonds       : angle       6.84176 (  129)
  SS BOND              : bond        0.00322 (    8)
  SS BOND              : angle       2.16162 (   16)
  covalent geometry    : bond        0.00287 ( 3625)
  covalent geometry    : angle       0.73319 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8507 (pm20) cc_final: 0.7415 (tp30)
REVERT: B  354 ASN cc_start: 0.9336 (t0) cc_final: 0.8950 (t0)
REVERT: B  356 LYS cc_start: 0.9392 (tppt) cc_final: 0.8975 (tppt)
REVERT: B  388 ASN cc_start: 0.7215 (t0) cc_final: 0.6872 (m110)
REVERT: B  403 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7453 (mpp80)
REVERT: D  340 GLU cc_start: 0.9136 (mp0) cc_final: 0.8836 (mp0)
REVERT: D  358 ILE cc_start: 0.8936 (mp) cc_final: 0.8694 (mp)
REVERT: D  394 ASN cc_start: 0.9192 (t0) cc_final: 0.8285 (p0)
REVERT: D  396 TYR cc_start: 0.8508 (m-80) cc_final: 0.7916 (m-80)
REVERT: D  402 ILE cc_start: 0.9041 (tp) cc_final: 0.8711 (tp)
REVERT: D  406 GLU cc_start: 0.8959 (pm20) cc_final: 0.8412 (pm20)
REVERT: D  409 GLN cc_start: 0.8973 (mt0) cc_final: 0.8686 (tt0)
REVERT: D  473 TYR cc_start: 0.8809 (t80) cc_final: 0.8452 (t80)
REVERT: D  506 GLN cc_start: 0.8356 (mt0) cc_final: 0.7908 (mp10)
REVERT: D  509 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7804 (ttm170)
REVERT: D  516 GLU cc_start: 0.8241 (tp30) cc_final: 0.7460 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.2049
  time to fit residues: 27.6438
Evaluate side-chains
  87 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 22 optimal weight:    0.0020
   chunk 41 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 36 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.0790

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
D 474 GLN
D 487 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.113202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.095002 restraints weight = 13667.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.097754 restraints weight = 8477.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.099693 restraints weight = 5943.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.6228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3633  Z= 0.127
  Angle     :  0.728  11.381   4946  Z= 0.366
  Chirality :  0.046   0.219    509
  Planarity :  0.005   0.046    644
  Dihedral  :  5.615  21.610    492
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 15.76 %
    Favored  : 83.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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: -3.46 (0.38), residues: 425
  helix: -3.12 (0.58), residues: 48
  sheet: -1.23 (0.56), residues: 75
  loop : -2.64 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 436 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.018   0.002   PHE D 400 
 TYR   0.014   0.001   TYR D 421 
 ARG   0.006   0.001   ARG B 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03179 (   53)
  hydrogen bonds       : angle       6.78010 (  129)
  SS BOND              : bond        0.00316 (    8)
  SS BOND              : angle       1.61643 (   16)
  covalent geometry    : bond        0.00282 ( 3625)
  covalent geometry    : angle       0.72352 ( 4930)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1610.08 seconds
wall clock time: 28 minutes 34.65 seconds (1714.65 seconds total)