Starting phenix.real_space_refine
on Thu Mar  6 03:20:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7the_25893/03_2025/7the_25893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7the_25893/03_2025/7the_25893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7the_25893/03_2025/7the_25893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7the_25893/03_2025/7the_25893.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7the_25893/03_2025/7the_25893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7the_25893/03_2025/7the_25893.cif"
  }
  resolution = 3.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1543 atoms to isotropic.
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      17      5.16       5
     C    2098      2.51       5
     N     549      2.21       5
     O     641      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3305
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 945
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "C"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 803
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.39, per 1000 atoms: 1.03
  Number of scatterers: 3305
  At special positions: 0
  Unit cell: (65.596, 81.466, 87.814, 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      17     16.00
     O     641      8.00
     N     549      7.00
     C    2098      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  92 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " 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
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 343 "
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 407.1 milliseconds
  

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  778

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 9 sheets defined
      12.5% alpha, 31.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.981A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 4.706A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 4.854A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ALA A 411 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'B' and resid 73 through 75
      No H-bonds generated for 'chain 'B' and resid 73 through 75'
    Processing helix  chain 'C' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 335
      removed outlier: 7.513A  pdb=" N   ASN A 334 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.975A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.378A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ILE B  34 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   ARG B  50 " --> pdb=" O   ILE B  34 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP B  36 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.378A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL B 102 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.730A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)

    109 hydrogen bonds defined for protein.
    252 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: 1.33

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 928
        1.33 -     1.45: 657
        1.45 -     1.57: 1781
        1.57 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 3388
  Sorted by residual:
  bond pdb=" C5  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.482 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" CZ  ARG B  94 "
       pdb=" NH2 ARG B  94 "
    ideal  model  delta    sigma   weight residual
    1.330  1.287  0.043 1.30e-02 5.92e+03 1.10e+01
  bond pdb=" CZ  ARG A 509 "
       pdb=" NH2 ARG A 509 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.04e+01
  bond pdb=" CZ  ARG A 457 "
       pdb=" NH2 ARG A 457 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG A 357 "
       pdb=" NH2 ARG A 357 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.02e+01
  ... (remaining 3383 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 3171
        1.82 -     3.63: 1161
        3.63 -     5.45: 247
        5.45 -     7.26: 22
        7.26 -     9.08: 4
  Bond angle restraints: 4605
  Sorted by residual:
  angle pdb=" CA  PHE A 347 "
        pdb=" CB  PHE A 347 "
        pdb=" CG  PHE A 347 "
      ideal   model   delta    sigma   weight residual
     113.80  119.35   -5.55 1.00e+00 1.00e+00 3.08e+01
  angle pdb=" N   CYS A 361 "
        pdb=" CA  CYS A 361 "
        pdb=" C   CYS A 361 "
      ideal   model   delta    sigma   weight residual
     108.79  117.19   -8.40 1.53e+00 4.27e-01 3.01e+01
  angle pdb=" C   THR A 393 "
        pdb=" N   ASN A 394 "
        pdb=" CA  ASN A 394 "
      ideal   model   delta    sigma   weight residual
     121.75  130.83   -9.08 1.73e+00 3.34e-01 2.75e+01
  angle pdb=" CA  ASP A 405 "
        pdb=" CB  ASP A 405 "
        pdb=" CG  ASP A 405 "
      ideal   model   delta    sigma   weight residual
     112.60  117.25   -4.65 1.00e+00 1.00e+00 2.16e+01
  angle pdb=" CA  ASP C  70 "
        pdb=" CB  ASP C  70 "
        pdb=" CG  ASP C  70 "
      ideal   model   delta    sigma   weight residual
     112.60  117.16   -4.56 1.00e+00 1.00e+00 2.08e+01
  ... (remaining 4600 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 1841
       16.95 -    33.89: 139
       33.89 -    50.84: 30
       50.84 -    67.79: 8
       67.79 -    84.73: 4
  Dihedral angle restraints: 2022
    sinusoidal: 794
      harmonic: 1228
  Sorted by residual:
  dihedral pdb=" CA  ARG B  83 "
           pdb=" C   ARG B  83 "
           pdb=" N   SER B  84 "
           pdb=" CA  SER B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.24   28.76     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  TYR B  32 "
           pdb=" C   TYR B  32 "
           pdb=" N   ALA B  33 "
           pdb=" CA  ALA B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.82   28.18     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  TYR B  91 "
           pdb=" C   TYR B  91 "
           pdb=" N   CYS B  92 "
           pdb=" CA  CYS B  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.36   27.64     0      5.00e+00 4.00e-02 3.06e+01
  ... (remaining 2019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 270
       0.076 -    0.152: 164
       0.152 -    0.228: 49
       0.228 -    0.303: 10
       0.303 -    0.379: 6
  Chirality restraints: 499
  Sorted by residual:
  chirality pdb=" CA  ALA A 520 "
            pdb=" N   ALA A 520 "
            pdb=" C   ALA A 520 "
            pdb=" CB  ALA A 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.11    0.38 2.00e-01 2.50e+01 3.60e+00
  chirality pdb=" CA  ARG B  83 "
            pdb=" N   ARG B  83 "
            pdb=" C   ARG B  83 "
            pdb=" CB  ARG B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" CA  LEU A 455 "
            pdb=" N   LEU A 455 "
            pdb=" C   LEU A 455 "
            pdb=" CB  LEU A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.86e+00
  ... (remaining 496 not shown)

  Planarity restraints: 595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  47 "   -0.113 2.00e-02 2.50e+03   5.99e-02 8.96e+01
        pdb=" CG  TRP B  47 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  47 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  47 "    0.069 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  47 "    0.035 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  47 "    0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  47 "    0.087 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  47 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  47 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  47 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 103 "    0.104 2.00e-02 2.50e+03   5.15e-02 6.64e+01
        pdb=" CG  TRP B 103 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 103 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 103 "   -0.039 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 103 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 103 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 103 "   -0.070 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 103 "    0.056 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 103 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 103 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 351 "    0.102 2.00e-02 2.50e+03   5.49e-02 6.03e+01
        pdb=" CG  TYR A 351 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 351 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 351 "   -0.039 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 351 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 351 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 351 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 351 "    0.085 2.00e-02 2.50e+03
  ... (remaining 592 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 1818
        3.02 -     3.49: 3232
        3.49 -     3.96: 5382
        3.96 -     4.43: 5919
        4.43 -     4.90: 9826
  Nonbonded interactions: 26177
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 442 "
            pdb=" OH  TYR A 451 "
     model   vdw
     2.548 3.040
  nonbonded pdb=" OD1 ASP A 467 "
            pdb=" OG  SER A 469 "
     model   vdw
     2.565 3.040
  nonbonded pdb=" OE2 GLU A 484 "
            pdb=" OH  TYR B  95 "
     model   vdw
     2.566 3.040
  nonbonded pdb=" OH  TYR B 100B"
            pdb=" OD1 ASN C  34 "
     model   vdw
     2.569 3.040
  nonbonded pdb=" OE2 GLU A 406 "
            pdb=" OH  TYR A 495 "
     model   vdw
     2.588 3.040
  ... (remaining 26172 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.380
  Find NCS groups from input model:        0.040
  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:             0.000
  Load rotamer database and sin/cos tables:3.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
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      :  0.013   0.069   3388  Z= 0.844
  Angle     :  1.877   9.080   4605  Z= 1.234
  Chirality :  0.106   0.379    499
  Planarity :  0.015   0.104    594
  Dihedral  : 13.764  84.731   1226
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 0.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -2.01 (0.39), residues: 417
  helix: -4.02 (0.48), residues: 40
  sheet:  0.21 (0.50), residues: 117
  loop : -1.70 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.113   0.029   TRP B  47 
 HIS   0.007   0.004   HIS A 519 
 PHE   0.062   0.013   PHE B  54 
 TYR   0.102   0.022   TYR A 351 
 ARG   0.015   0.002   ARG A 346 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7767 (p-90) cc_final: 0.7518 (p-90)
REVERT: A  484 GLU cc_start: 0.8295 (pm20) cc_final: 0.7878 (pm20)
REVERT: A  493 GLN cc_start: 0.8765 (tt0) cc_final: 0.8364 (tt0)
REVERT: A  506 GLN cc_start: 0.7602 (mt0) cc_final: 0.7191 (mt0)
REVERT: B   36 TRP cc_start: 0.9068 (m100) cc_final: 0.8253 (m-10)
REVERT: B   48 MET cc_start: 0.8169 (mtp) cc_final: 0.7521 (mtm)
REVERT: B   56 ILE cc_start: 0.8594 (mt) cc_final: 0.8365 (tt)
REVERT: B  105 GLN cc_start: 0.8720 (tt0) cc_final: 0.8165 (pt0)
REVERT: C   34 ASN cc_start: 0.8908 (m-40) cc_final: 0.7510 (m-40)
REVERT: C   89 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7010 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2052
  time to fit residues: 30.3196
Evaluate side-chains
  90 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   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 501 ASN
B  58 ASN
** B  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.115099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.102719 restraints weight = 8826.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.105617 restraints weight = 4609.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.107508 restraints weight = 2850.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3388  Z= 0.246
  Angle     :  0.723   6.328   4605  Z= 0.391
  Chirality :  0.048   0.166    499
  Planarity :  0.005   0.036    594
  Dihedral  :  7.512  55.944    489
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 12.74 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.39), residues: 417
  helix: -3.35 (0.68), residues: 35
  sheet:  0.09 (0.45), residues: 138
  loop : -1.30 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.021   0.002   PHE C  98 
 TYR   0.020   0.002   TYR A 365 
 ARG   0.005   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7148 (ttp-110)
REVERT: A  406 GLU cc_start: 0.8422 (pt0) cc_final: 0.7431 (pt0)
REVERT: A  467 ASP cc_start: 0.7647 (t0) cc_final: 0.6459 (p0)
REVERT: A  468 ILE cc_start: 0.9153 (pt) cc_final: 0.8925 (pt)
REVERT: B   36 TRP cc_start: 0.9015 (m100) cc_final: 0.8095 (m-10)
REVERT: B   48 MET cc_start: 0.8105 (mtp) cc_final: 0.7520 (mtm)
REVERT: B   96 MET cc_start: 0.8112 (mtp) cc_final: 0.7793 (mmm)
REVERT: B  105 GLN cc_start: 0.8720 (tt0) cc_final: 0.8145 (pt0)
  outliers start: 11
  outliers final: 9
  residues processed: 104
  average time/residue: 0.1830
  time to fit residues: 22.4995
Evaluate side-chains
  95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.115291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.103123 restraints weight = 8589.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.106053 restraints weight = 4465.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.107957 restraints weight = 2738.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3388  Z= 0.237
  Angle     :  0.654   6.978   4605  Z= 0.349
  Chirality :  0.045   0.159    499
  Planarity :  0.005   0.048    594
  Dihedral  :  6.951  55.933    489
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 16.07 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.40), residues: 417
  helix: -3.03 (0.75), residues: 35
  sheet:  0.01 (0.41), residues: 150
  loop : -1.08 (0.40), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 436 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.009   0.001   PHE A 464 
 TYR   0.013   0.002   TYR A 365 
 ARG   0.009   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7627 (m110) cc_final: 0.7217 (m110)
REVERT: A  467 ASP cc_start: 0.7406 (t0) cc_final: 0.6501 (p0)
REVERT: B   32 TYR cc_start: 0.8419 (m-10) cc_final: 0.7956 (m-10)
REVERT: B   36 TRP cc_start: 0.9072 (m100) cc_final: 0.8199 (m-10)
REVERT: B   48 MET cc_start: 0.8128 (mtp) cc_final: 0.7375 (mtm)
REVERT: B   61 GLN cc_start: 0.8917 (pm20) cc_final: 0.8358 (pp30)
REVERT: B   96 MET cc_start: 0.8297 (mtp) cc_final: 0.8007 (mmt)
REVERT: B  105 GLN cc_start: 0.8696 (tt0) cc_final: 0.8258 (pt0)
REVERT: C   89 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7470 (tm-30)
  outliers start: 15
  outliers final: 13
  residues processed: 103
  average time/residue: 0.1777
  time to fit residues: 21.7104
Evaluate side-chains
  102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0980
   chunk 5 optimal weight:    0.0020
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0870
   overall best weight:    0.2766

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

Flipped N/Q/H residues before XYZ refinement:
C  55 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 = 0.119465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.107372 restraints weight = 8624.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.110246 restraints weight = 4423.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.112113 restraints weight = 2706.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3388  Z= 0.148
  Angle     :  0.595   7.064   4605  Z= 0.315
  Chirality :  0.044   0.155    499
  Planarity :  0.005   0.043    594
  Dihedral  :  6.304  54.516    489
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.01 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 (0.41), residues: 417
  helix: -2.97 (0.76), residues: 35
  sheet:  0.21 (0.41), residues: 151
  loop : -0.71 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.008   0.001   PHE C  62 
 TYR   0.016   0.001   TYR A 451 
 ARG   0.008   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7636 (m110) cc_final: 0.7165 (m110)
REVERT: A  406 GLU cc_start: 0.8366 (pt0) cc_final: 0.8159 (pt0)
REVERT: A  467 ASP cc_start: 0.6948 (t0) cc_final: 0.6370 (p0)
REVERT: B   36 TRP cc_start: 0.8923 (m100) cc_final: 0.8446 (m100)
REVERT: B   48 MET cc_start: 0.8161 (mtp) cc_final: 0.7455 (mtm)
REVERT: B   61 GLN cc_start: 0.8804 (pm20) cc_final: 0.8276 (pp30)
REVERT: B  105 GLN cc_start: 0.8677 (tt0) cc_final: 0.8183 (pt0)
REVERT: C   31 ASN cc_start: 0.7750 (m-40) cc_final: 0.7141 (t0)
REVERT: C   89 GLN cc_start: 0.8252 (tm-30) cc_final: 0.8005 (tm-30)
  outliers start: 11
  outliers final: 10
  residues processed: 103
  average time/residue: 0.1686
  time to fit residues: 20.8285
Evaluate side-chains
  95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0770
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.116534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.104280 restraints weight = 8630.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.107125 restraints weight = 4496.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.108977 restraints weight = 2778.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.4127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3388  Z= 0.210
  Angle     :  0.632   6.815   4605  Z= 0.330
  Chirality :  0.045   0.187    499
  Planarity :  0.005   0.049    594
  Dihedral  :  6.369  55.567    489
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 16.07 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 (0.41), residues: 417
  helix: -2.67 (0.74), residues: 41
  sheet:  0.15 (0.41), residues: 152
  loop : -0.64 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 436 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.009   0.001   PHE C  62 
 TYR   0.014   0.002   TYR A 365 
 ARG   0.005   0.001   ARG A 403 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7684 (m110) cc_final: 0.7231 (m110)
REVERT: A  406 GLU cc_start: 0.8512 (pt0) cc_final: 0.8200 (pt0)
REVERT: A  423 TYR cc_start: 0.7589 (t80) cc_final: 0.7329 (t80)
REVERT: A  467 ASP cc_start: 0.7122 (t0) cc_final: 0.6251 (p0)
REVERT: B   36 TRP cc_start: 0.9045 (m100) cc_final: 0.8561 (m100)
REVERT: B   48 MET cc_start: 0.8119 (mtp) cc_final: 0.7430 (mtm)
REVERT: B   82 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7096 (pp)
REVERT: B  105 GLN cc_start: 0.8694 (tt0) cc_final: 0.8155 (pt0)
REVERT: C   89 GLN cc_start: 0.8274 (tm-30) cc_final: 0.8033 (tm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 102
  average time/residue: 0.1578
  time to fit residues: 19.4771
Evaluate side-chains
  95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0870
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.116509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.104115 restraints weight = 9003.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.106970 restraints weight = 4622.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.108851 restraints weight = 2850.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.4315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3388  Z= 0.203
  Angle     :  0.634   6.885   4605  Z= 0.333
  Chirality :  0.045   0.187    499
  Planarity :  0.005   0.049    594
  Dihedral  :  6.291  55.349    489
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 17.17 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 (0.41), residues: 417
  helix: -2.67 (0.75), residues: 41
  sheet:  0.26 (0.42), residues: 148
  loop : -0.69 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 436 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.008   0.001   PHE C  62 
 TYR   0.016   0.001   TYR A 365 
 ARG   0.008   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7633 (m110) cc_final: 0.7236 (m110)
REVERT: A  406 GLU cc_start: 0.8468 (pt0) cc_final: 0.8162 (pt0)
REVERT: A  423 TYR cc_start: 0.7602 (t80) cc_final: 0.7362 (t80)
REVERT: A  467 ASP cc_start: 0.7010 (t0) cc_final: 0.6279 (p0)
REVERT: B   36 TRP cc_start: 0.9028 (m100) cc_final: 0.8536 (m-10)
REVERT: B   48 MET cc_start: 0.8097 (mtp) cc_final: 0.7413 (mtm)
REVERT: B   82 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7157 (pp)
REVERT: B  105 GLN cc_start: 0.8661 (tt0) cc_final: 0.8149 (pt0)
REVERT: C   89 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8104 (tm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 96
  average time/residue: 0.1479
  time to fit residues: 18.1241
Evaluate side-chains
  100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    0.2980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.116502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.104200 restraints weight = 8647.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.107008 restraints weight = 4497.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108864 restraints weight = 2791.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3388  Z= 0.206
  Angle     :  0.623   6.782   4605  Z= 0.332
  Chirality :  0.044   0.175    499
  Planarity :  0.005   0.050    594
  Dihedral  :  6.252  55.083    489
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 17.17 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.95 (0.41), residues: 417
  helix: -2.76 (0.68), residues: 47
  sheet:  0.16 (0.42), residues: 149
  loop : -0.62 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 436 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.008   0.001   PHE C  62 
 TYR   0.017   0.001   TYR A 365 
 ARG   0.008   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7630 (m110) cc_final: 0.7238 (m110)
REVERT: A  406 GLU cc_start: 0.8489 (pt0) cc_final: 0.8188 (pt0)
REVERT: A  423 TYR cc_start: 0.7567 (t80) cc_final: 0.7320 (t80)
REVERT: A  467 ASP cc_start: 0.7156 (t0) cc_final: 0.6389 (p0)
REVERT: B   36 TRP cc_start: 0.9060 (m100) cc_final: 0.8719 (m-10)
REVERT: B   82 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7142 (pp)
REVERT: B  105 GLN cc_start: 0.8727 (tt0) cc_final: 0.8229 (pt0)
REVERT: C   31 ASN cc_start: 0.7688 (m-40) cc_final: 0.7036 (t0)
  outliers start: 20
  outliers final: 18
  residues processed: 98
  average time/residue: 0.1360
  time to fit residues: 16.7935
Evaluate side-chains
  102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0270
   chunk 1 optimal weight:    0.0570
   chunk 19 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0870
   overall best weight:    0.3334

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.119788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.107861 restraints weight = 8688.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.110541 restraints weight = 4525.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.112396 restraints weight = 2817.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.4648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3388  Z= 0.162
  Angle     :  0.603   6.653   4605  Z= 0.319
  Chirality :  0.044   0.179    499
  Planarity :  0.005   0.051    594
  Dihedral  :  6.019  54.416    489
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 18.84 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.85 (0.42), residues: 417
  helix: -2.70 (0.70), residues: 47
  sheet:  0.29 (0.42), residues: 148
  loop : -0.60 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.008   0.001   PHE C  62 
 TYR   0.010   0.001   TYR B 100C
 ARG   0.007   0.001   ARG A 403 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7556 (m110) cc_final: 0.7204 (m110)
REVERT: A  403 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7438 (ttp80)
REVERT: A  406 GLU cc_start: 0.8313 (pt0) cc_final: 0.8057 (pt0)
REVERT: A  467 ASP cc_start: 0.7058 (t70) cc_final: 0.6388 (p0)
REVERT: B   82 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7072 (pp)
REVERT: B   96 MET cc_start: 0.8415 (mmm) cc_final: 0.8145 (mmm)
REVERT: B  105 GLN cc_start: 0.8634 (tt0) cc_final: 0.8169 (pt0)
REVERT: C   31 ASN cc_start: 0.7501 (m-40) cc_final: 0.7025 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 97
  average time/residue: 0.1295
  time to fit residues: 15.6835
Evaluate side-chains
  100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    0.0040
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 35 optimal weight:    0.3980
   overall best weight:    0.4992

-------------------------------------------------------------------------------
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 = 0.3722 r_free = 0.3722 target = 0.118804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.106915 restraints weight = 8720.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.109651 restraints weight = 4533.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.111476 restraints weight = 2809.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3388  Z= 0.191
  Angle     :  0.625   6.270   4605  Z= 0.333
  Chirality :  0.045   0.197    499
  Planarity :  0.005   0.053    594
  Dihedral  :  6.091  54.662    489
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.39 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 (0.41), residues: 417
  helix: -2.76 (0.68), residues: 47
  sheet:  0.25 (0.42), residues: 148
  loop : -0.61 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  36 
 HIS   0.002   0.002   HIS A 519 
 PHE   0.009   0.001   PHE C  62 
 TYR   0.010   0.001   TYR B 100C
 ARG   0.007   0.001   ARG A 403 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7575 (m110) cc_final: 0.7192 (m110)
REVERT: A  403 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7469 (ttp80)
REVERT: A  406 GLU cc_start: 0.8365 (pt0) cc_final: 0.8052 (pt0)
REVERT: A  423 TYR cc_start: 0.7361 (t80) cc_final: 0.6928 (t80)
REVERT: A  467 ASP cc_start: 0.7174 (t70) cc_final: 0.6472 (p0)
REVERT: B   48 MET cc_start: 0.8218 (mtp) cc_final: 0.7991 (mtp)
REVERT: B   77 THR cc_start: 0.7918 (m) cc_final: 0.7545 (p)
REVERT: B   82 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7196 (pp)
REVERT: B   96 MET cc_start: 0.8461 (mmm) cc_final: 0.8183 (mmm)
REVERT: B  105 GLN cc_start: 0.8653 (tt0) cc_final: 0.8176 (pt0)
REVERT: C   31 ASN cc_start: 0.7492 (m-40) cc_final: 0.7033 (t0)
REVERT: C   36 TYR cc_start: 0.8746 (m-80) cc_final: 0.7946 (m-80)
  outliers start: 15
  outliers final: 14
  residues processed: 94
  average time/residue: 0.1283
  time to fit residues: 15.2347
Evaluate side-chains
  100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.116188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.104104 restraints weight = 8716.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.106910 restraints weight = 4570.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108689 restraints weight = 2826.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3388  Z= 0.236
  Angle     :  0.644   6.081   4605  Z= 0.345
  Chirality :  0.045   0.196    499
  Planarity :  0.005   0.050    594
  Dihedral  :  6.305  55.413    489
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 21.33 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.41), residues: 417
  helix: -2.82 (0.66), residues: 47
  sheet:  0.22 (0.41), residues: 154
  loop : -0.81 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP B  36 
 HIS   0.004   0.003   HIS A 519 
 PHE   0.009   0.001   PHE A 464 
 TYR   0.009   0.001   TYR B  95 
 ARG   0.008   0.001   ARG B  94 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7630 (m110) cc_final: 0.7245 (m110)
REVERT: A  406 GLU cc_start: 0.8509 (pt0) cc_final: 0.8169 (pt0)
REVERT: A  467 ASP cc_start: 0.7223 (t70) cc_final: 0.6553 (p0)
REVERT: B   48 MET cc_start: 0.8205 (mtp) cc_final: 0.7913 (mtp)
REVERT: B   77 THR cc_start: 0.7940 (m) cc_final: 0.7572 (p)
REVERT: B   82 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7188 (pp)
REVERT: B  105 GLN cc_start: 0.8786 (tt0) cc_final: 0.8283 (pt0)
REVERT: C   31 ASN cc_start: 0.7586 (m-40) cc_final: 0.7033 (t0)
  outliers start: 15
  outliers final: 14
  residues processed: 94
  average time/residue: 0.1284
  time to fit residues: 15.2899
Evaluate side-chains
  99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.116761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.104589 restraints weight = 8874.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.107423 restraints weight = 4650.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.109224 restraints weight = 2861.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.4792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3388  Z= 0.215
  Angle     :  0.642   6.614   4605  Z= 0.343
  Chirality :  0.045   0.200    499
  Planarity :  0.005   0.052    594
  Dihedral  :  6.267  55.001    489
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 20.78 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.41), residues: 417
  helix: -2.81 (0.67), residues: 47
  sheet:  0.17 (0.41), residues: 154
  loop : -0.85 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B  36 
 HIS   0.004   0.002   HIS A 519 
 PHE   0.008   0.001   PHE C  62 
 TYR   0.014   0.001   TYR C  92 
 ARG   0.008   0.001   ARG A 403 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1606.94 seconds
wall clock time: 28 minutes 30.54 seconds (1710.54 seconds total)