Starting phenix.real_space_refine
on Thu Mar  6 05:02:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y4s_33606/03_2025/7y4s_33606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y4s_33606/03_2025/7y4s_33606.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y4s_33606/03_2025/7y4s_33606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y4s_33606/03_2025/7y4s_33606.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y4s_33606/03_2025/7y4s_33606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y4s_33606/03_2025/7y4s_33606.cif"
  }
  resolution = 3.5
  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=  -0.000 sd=   0.097
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      12      5.16       5
     C    3126      2.51       5
     N     912      2.21       5
     O     890      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4940
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2470
          Classifications: {'peptide': 343}
          Incomplete info: {'truncation_to_alanine': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 319}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 264
          Unresolved non-hydrogen angles: 324
          Unresolved non-hydrogen dihedrals: 214
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 149
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.04, per 1000 atoms: 0.82
  Number of scatterers: 4940
  At special positions: 0
  Unit cell: (103.455, 176.605, 83.6, 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      12     16.00
     O     890      8.00
     N     912      7.00
     C    3126      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 597.3 milliseconds
  

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1288

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 6 sheets defined
      40.4% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 125 through 228
      Proline residue:  A 134  - end of helix
    Processing helix  chain 'A' and resid 235 through 254
      removed outlier: 4.212A  pdb=" N   CYS A 242 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LEU A 243 " --> pdb=" O   MET A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 285
      removed outlier: 3.749A  pdb=" N   PHE A 281 " --> pdb=" O   TRP A 277 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ARG A 282 " --> pdb=" O   ARG A 278 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 228
      Proline residue:  B 134  - end of helix
    Processing helix  chain 'B' and resid 235 through 254
      removed outlier: 4.212A  pdb=" N   CYS B 242 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU B 243 " --> pdb=" O   MET B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 285
      removed outlier: 3.749A  pdb=" N   PHE B 281 " --> pdb=" O   TRP B 277 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ARG B 282 " --> pdb=" O   ARG B 278 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA B 283 " --> pdb=" O   LYS B 279 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 302 through 304
      removed outlier: 3.556A  pdb=" N   VAL A 311 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU A 467 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   LEU A 424 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ALA A 440 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   PHE A 426 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 386
    Processing sheet with id=AA4, first strand: chain 'B' and resid 302 through 304
      removed outlier: 3.556A  pdb=" N   VAL B 311 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU B 467 " --> pdb=" O   VAL B 311 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   LEU B 424 " --> pdb=" O   ALA B 440 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ALA B 440 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   PHE B 426 " --> pdb=" O   LEU B 438 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 333 through 335
    Processing sheet with id=AA6, first strand: chain 'B' and resid 385 through 386

    299 hydrogen bonds defined for protein.
    873 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: 1.23

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1722
        1.34 -     1.46: 918
        1.46 -     1.58: 2394
        1.58 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 5052
  Sorted by residual:
  bond pdb=" CB  VAL A 375 "
       pdb=" CG1 VAL A 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.99e+00
  bond pdb=" CB  VAL B 375 "
       pdb=" CG1 VAL B 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.98e+00
  bond pdb=" CB  VAL A 375 "
       pdb=" CG2 VAL A 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.86e+00
  bond pdb=" CB  VAL B 375 "
       pdb=" CG2 VAL B 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.86e+00
  bond pdb=" CA  PRO B 448 "
       pdb=" C   PRO B 448 "
    ideal  model  delta    sigma   weight residual
    1.524  1.553 -0.029 2.00e-02 2.50e+03 2.03e+00
  ... (remaining 5047 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 6624
        1.62 -     3.24: 203
        3.24 -     4.87: 51
        4.87 -     6.49: 12
        6.49 -     8.11: 4
  Bond angle restraints: 6894
  Sorted by residual:
  angle pdb=" C   VAL B 375 "
        pdb=" CA  VAL B 375 "
        pdb=" CB  VAL B 375 "
      ideal   model   delta    sigma   weight residual
     109.33  112.78   -3.45 9.80e-01 1.04e+00 1.24e+01
  angle pdb=" C   ASP B 459 "
        pdb=" N   LYS B 460 "
        pdb=" CA  LYS B 460 "
      ideal   model   delta    sigma   weight residual
     121.54  127.67   -6.13 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" C   ASP A 459 "
        pdb=" N   LYS A 460 "
        pdb=" CA  LYS A 460 "
      ideal   model   delta    sigma   weight residual
     121.54  127.63   -6.09 1.91e+00 2.74e-01 1.02e+01
  angle pdb=" CA  VAL B 375 "
        pdb=" C   VAL B 375 "
        pdb=" N   PRO B 376 "
      ideal   model   delta    sigma   weight residual
     116.57  119.49   -2.92 9.80e-01 1.04e+00 8.90e+00
  angle pdb=" CA  ARG A 404 "
        pdb=" CB  ARG A 404 "
        pdb=" CG  ARG A 404 "
      ideal   model   delta    sigma   weight residual
     114.10  119.40   -5.30 2.00e+00 2.50e-01 7.02e+00
  ... (remaining 6889 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.14: 2762
       15.14 -    30.28: 216
       30.28 -    45.41: 50
       45.41 -    60.55: 8
       60.55 -    75.69: 8
  Dihedral angle restraints: 3044
    sinusoidal: 1066
      harmonic: 1978
  Sorted by residual:
  dihedral pdb=" CA  SER A 430 "
           pdb=" C   SER A 430 "
           pdb=" N   ASP A 431 "
           pdb=" CA  ASP A 431 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  SER B 430 "
           pdb=" C   SER B 430 "
           pdb=" N   ASP B 431 "
           pdb=" CA  ASP B 431 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CB  MET A 285 "
           pdb=" CG  MET A 285 "
           pdb=" SD  MET A 285 "
           pdb=" CE  MET A 285 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.60  -59.60     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 470
       0.031 -    0.061: 203
       0.061 -    0.092: 70
       0.092 -    0.122: 19
       0.122 -    0.153: 12
  Chirality restraints: 774
  Sorted by residual:
  chirality pdb=" CA  VAL B 395 "
            pdb=" N   VAL B 395 "
            pdb=" C   VAL B 395 "
            pdb=" CB  VAL B 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.85e-01
  chirality pdb=" CA  VAL A 395 "
            pdb=" N   VAL A 395 "
            pdb=" C   VAL A 395 "
            pdb=" CB  VAL A 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" CA  VAL B 304 "
            pdb=" N   VAL B 304 "
            pdb=" C   VAL B 304 "
            pdb=" CB  VAL B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 771 not shown)

  Planarity restraints: 928
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 399 "    0.042 5.00e-02 4.00e+02   6.45e-02 6.66e+00
        pdb=" N   PRO A 400 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 400 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 400 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 399 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.62e+00
        pdb=" N   PRO B 400 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO B 400 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 400 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 375 "   -0.036 5.00e-02 4.00e+02   5.42e-02 4.71e+00
        pdb=" N   PRO A 376 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 376 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 376 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 925 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 1698
        2.88 -     3.38: 4794
        3.38 -     3.89: 7875
        3.89 -     4.39: 8095
        4.39 -     4.90: 14623
  Nonbonded interactions: 37085
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 348 "
            pdb=" NH1 ARG B 412 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" OE1 GLU A 348 "
            pdb=" NH1 ARG A 412 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" O   THR A 292 "
            pdb=" N   HIS A 337 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" O   THR B 292 "
            pdb=" N   HIS B 337 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" OH  TYR A 346 "
            pdb=" OE2 GLU A 348 "
     model   vdw
     2.513 3.040
  ... (remaining 37080 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.540
  Find NCS groups from input model:        0.090
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
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   0.057   5052  Z= 0.276
  Angle     :  0.740   8.109   6894  Z= 0.383
  Chirality :  0.042   0.153    774
  Planarity :  0.008   0.064    928
  Dihedral  : 12.744  75.690   1756
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  2.30 %
    Favored  : 97.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.47 (0.31), residues: 678
  helix:  3.05 (0.26), residues: 276
  sheet: -0.87 (0.46), residues: 120
  loop : -0.26 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 277 
 HIS   0.001   0.000   HIS B 373 
 PHE   0.012   0.002   PHE A 426 
 TYR   0.006   0.002   TYR A 450 
 ARG   0.004   0.001   ARG B 404 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A  389 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8067 (mmtt)
REVERT: B  389 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8068 (mmtt)
  outliers start: 2
  outliers final: 1
  residues processed: 107
  average time/residue: 0.2482
  time to fit residues: 31.8754
Evaluate side-chains
  72 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  396 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0000
   chunk 34 optimal weight:   40.0000
   chunk 27 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0060
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0870
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN
** B 339 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 = 0.4073 r_free = 0.4073 target = 0.183052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.145882 restraints weight = 5684.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.141354 restraints weight = 6006.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.143773 restraints weight = 6514.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5052  Z= 0.184
  Angle     :  0.563   6.219   6894  Z= 0.281
  Chirality :  0.038   0.123    774
  Planarity :  0.006   0.054    928
  Dihedral  :  4.611  59.911    741
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  8.76 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.14 (0.33), residues: 678
  helix:  4.25 (0.29), residues: 246
  sheet: -0.90 (0.46), residues: 122
  loop :  0.07 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 347 
 HIS   0.002   0.001   HIS A 458 
 PHE   0.012   0.002   PHE B 452 
 TYR   0.004   0.001   TYR B 450 
 ARG   0.007   0.001   ARG B 207 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A  387 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7778 (mp0)
REVERT: A  398 LYS cc_start: 0.7400 (tptp) cc_final: 0.7119 (tptt)
REVERT: B  387 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7771 (mp0)
REVERT: B  398 LYS cc_start: 0.7371 (tptp) cc_final: 0.7116 (tptt)
  outliers start: 13
  outliers final: 2
  residues processed: 90
  average time/residue: 0.2936
  time to fit residues: 31.6100
Evaluate side-chains
  66 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 44 optimal weight:   50.0000
   chunk 30 optimal weight:    0.0670
   chunk 7 optimal weight:    2.9990
   chunk 46 optimal weight:   20.0000
   chunk 66 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.9122

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

Flipped N/Q/H residues before XYZ refinement:
A 327 GLN
A 338 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN
B 338 GLN
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.176685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139262 restraints weight = 5815.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.138067 restraints weight = 7278.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.140716 restraints weight = 6734.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   5052  Z= 0.304
  Angle     :  0.612   9.065   6894  Z= 0.296
  Chirality :  0.040   0.158    774
  Planarity :  0.006   0.050    928
  Dihedral  :  4.021  14.748    738
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.52 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.26 (0.33), residues: 678
  helix:  4.42 (0.30), residues: 246
  sheet: -1.40 (0.45), residues: 122
  loop :  0.35 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 347 
 HIS   0.002   0.000   HIS B 345 
 PHE   0.021   0.002   PHE B 293 
 TYR   0.005   0.001   TYR B 346 
 ARG   0.008   0.001   ARG B 198 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.586 
Fit side-chains
REVERT: A  285 MET cc_start: 0.8196 (mtt) cc_final: 0.7968 (mtt)
REVERT: A  387 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7725 (mp0)
REVERT: A  389 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8046 (mmtt)
  outliers start: 11
  outliers final: 9
  residues processed: 80
  average time/residue: 0.2197
  time to fit residues: 22.0463
Evaluate side-chains
  72 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 ASP
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 2 optimal weight:   20.0000
   chunk 26 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 34 optimal weight:   50.0000
   chunk 63 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN
** B 339 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 = 0.3996 r_free = 0.3996 target = 0.175765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.137115 restraints weight = 5979.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.135793 restraints weight = 6809.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.137701 restraints weight = 6831.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5052  Z= 0.271
  Angle     :  0.578   5.599   6894  Z= 0.283
  Chirality :  0.039   0.133    774
  Planarity :  0.005   0.049    928
  Dihedral  :  3.990  14.682    738
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 13.13 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.36 (0.33), residues: 678
  helix:  4.48 (0.30), residues: 246
  sheet: -1.51 (0.45), residues: 122
  loop :  0.51 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 347 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.016   0.002   PHE B 452 
 TYR   0.005   0.001   TYR A 450 
 ARG   0.005   0.000   ARG B 166 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A  389 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8117 (mmtt)
REVERT: B  389 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8092 (mmtt)
  outliers start: 18
  outliers final: 12
  residues processed: 79
  average time/residue: 0.2049
  time to fit residues: 20.4127
Evaluate side-chains
  73 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  396 GLU
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0010
   chunk 55 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:   50.0000
   chunk 8 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN
** B 339 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 = 0.4069 r_free = 0.4069 target = 0.182273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.146240 restraints weight = 5765.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.143967 restraints weight = 6573.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.145391 restraints weight = 6952.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5052  Z= 0.193
  Angle     :  0.549   5.468   6894  Z= 0.270
  Chirality :  0.039   0.126    774
  Planarity :  0.005   0.048    928
  Dihedral  :  3.865  14.295    738
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 14.98 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.42 (0.34), residues: 678
  helix:  4.51 (0.29), residues: 246
  sheet: -1.30 (0.45), residues: 128
  loop :  0.53 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 347 
 HIS   0.001   0.000   HIS A 337 
 PHE   0.014   0.002   PHE B 182 
 TYR   0.003   0.001   TYR B 450 
 ARG   0.005   0.000   ARG A 166 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.597 
Fit side-chains
REVERT: A  285 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7717 (mtt)
  outliers start: 21
  outliers final: 7
  residues processed: 81
  average time/residue: 0.2571
  time to fit residues: 25.6248
Evaluate side-chains
  68 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    9.9990
   chunk 10 optimal weight:    0.4980
   chunk 60 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 338 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 264 GLN
B 338 GLN
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.177925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.143161 restraints weight = 5813.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.138315 restraints weight = 6886.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.140675 restraints weight = 7587.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   5052  Z= 0.321
  Angle     :  0.595   5.171   6894  Z= 0.292
  Chirality :  0.039   0.126    774
  Planarity :  0.005   0.047    928
  Dihedral  :  4.011  14.806    738
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 15.44 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.41 (0.34), residues: 678
  helix:  4.52 (0.29), residues: 246
  sheet: -1.66 (0.45), residues: 122
  loop :  0.64 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 347 
 HIS   0.001   0.000   HIS B 299 
 PHE   0.019   0.002   PHE B 452 
 TYR   0.006   0.001   TYR B 427 
 ARG   0.005   0.000   ARG B 166 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.581 
Fit side-chains
REVERT: A  285 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7809 (mtt)
REVERT: B  285 MET cc_start: 0.8033 (mtt) cc_final: 0.7782 (mtt)
  outliers start: 18
  outliers final: 13
  residues processed: 73
  average time/residue: 0.2267
  time to fit residues: 20.9167
Evaluate side-chains
  73 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  431 ASP
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 47 optimal weight:    8.9990
   chunk 25 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0770
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
B 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.179072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.144750 restraints weight = 5662.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.141516 restraints weight = 7119.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.144099 restraints weight = 7753.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5052  Z= 0.246
  Angle     :  0.569   6.235   6894  Z= 0.278
  Chirality :  0.038   0.128    774
  Planarity :  0.005   0.047    928
  Dihedral  :  3.943  15.218    738
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.44 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.46 (0.34), residues: 678
  helix:  4.58 (0.29), residues: 246
  sheet: -1.65 (0.45), residues: 122
  loop :  0.66 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 347 
 HIS   0.001   0.000   HIS B 337 
 PHE   0.014   0.002   PHE B 452 
 TYR   0.003   0.001   TYR B 450 
 ARG   0.005   0.000   ARG A 166 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.641 
Fit side-chains
REVERT: B  285 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7789 (mtt)
  outliers start: 17
  outliers final: 12
  residues processed: 75
  average time/residue: 0.2222
  time to fit residues: 20.9111
Evaluate side-chains
  74 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  353 ASP
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 50 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:   20.0000
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 339 GLN
B 264 GLN
B 339 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.178447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.143568 restraints weight = 5774.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.140680 restraints weight = 6591.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.141250 restraints weight = 7392.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5052  Z= 0.275
  Angle     :  0.580   5.635   6894  Z= 0.284
  Chirality :  0.039   0.133    774
  Planarity :  0.005   0.046    928
  Dihedral  :  3.958  15.282    738
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 16.82 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.45 (0.34), residues: 678
  helix:  4.55 (0.29), residues: 246
  sheet: -1.70 (0.45), residues: 122
  loop :  0.70 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 347 
 HIS   0.001   0.000   HIS B 156 
 PHE   0.017   0.002   PHE B 182 
 TYR   0.003   0.001   TYR B 450 
 ARG   0.005   0.000   ARG A 166 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.549 
Fit side-chains
REVERT: B  285 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7794 (mtt)
  outliers start: 16
  outliers final: 14
  residues processed: 76
  average time/residue: 0.2340
  time to fit residues: 22.1759
Evaluate side-chains
  75 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  431 ASP
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 36 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 0 optimal weight:   50.0000
   chunk 52 optimal weight:    0.1980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
B 339 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.179464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.144513 restraints weight = 5711.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.141382 restraints weight = 7514.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.143855 restraints weight = 8229.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5052  Z= 0.255
  Angle     :  0.571   6.035   6894  Z= 0.280
  Chirality :  0.038   0.128    774
  Planarity :  0.005   0.047    928
  Dihedral  :  3.923  15.430    738
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.90 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.43 (0.34), residues: 678
  helix:  4.55 (0.29), residues: 246
  sheet: -1.68 (0.45), residues: 122
  loop :  0.65 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 347 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.016   0.002   PHE B 182 
 TYR   0.004   0.001   TYR B 450 
 ARG   0.007   0.000   ARG B 404 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  285 MET cc_start: 0.7806 (mtt) cc_final: 0.7554 (mtt)
REVERT: B  285 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7754 (mtt)
  outliers start: 16
  outliers final: 13
  residues processed: 76
  average time/residue: 0.2614
  time to fit residues: 24.5009
Evaluate side-chains
  77 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  431 ASP
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 45 optimal weight:    6.9990
   chunk 52 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0980
   chunk 10 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0170
   overall best weight:    0.3218

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.182282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.146809 restraints weight = 5728.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.146790 restraints weight = 7767.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.149959 restraints weight = 7591.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5052  Z= 0.178
  Angle     :  0.558   6.195   6894  Z= 0.275
  Chirality :  0.038   0.125    774
  Planarity :  0.005   0.048    928
  Dihedral  :  3.797  15.234    738
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.82 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.45 (0.34), residues: 678
  helix:  4.58 (0.29), residues: 246
  sheet: -1.61 (0.45), residues: 122
  loop :  0.62 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 347 
 HIS   0.001   0.000   HIS B 458 
 PHE   0.015   0.002   PHE A 182 
 TYR   0.004   0.001   TYR B 450 
 ARG   0.006   0.000   ARG A 166 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.959 
Fit side-chains
REVERT: B  285 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7652 (mtt)
  outliers start: 12
  outliers final: 8
  residues processed: 77
  average time/residue: 0.2341
  time to fit residues: 22.3543
Evaluate side-chains
  74 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7715 > 50:
  distance: 99 - 103:   9.375
  distance: 103 - 104:  20.809
  distance: 104 - 105:  13.330
  distance: 104 - 107:   8.507
  distance: 105 - 106:  15.345
  distance: 105 - 114:  11.112
  distance: 107 - 108:  17.682
  distance: 108 - 109:  14.012
  distance: 108 - 110:  24.746
  distance: 109 - 111:  20.624
  distance: 110 - 112:  12.173
  distance: 114 - 115:  11.483
  distance: 115 - 116:  26.522
  distance: 115 - 118:  13.239
  distance: 116 - 117:  20.374
  distance: 116 - 119:  26.633
  distance: 119 - 120:  17.769
  distance: 120 - 121:  11.201
  distance: 120 - 123:  10.980
  distance: 121 - 122:  33.204
  distance: 123 - 124:  35.386
  distance: 124 - 126:  19.878
  distance: 125 - 127:  19.747
  distance: 128 - 129:   4.734
  distance: 130 - 131:  25.258
  distance: 131 - 132:  28.986
  distance: 131 - 134:  40.658
  distance: 132 - 133:  29.779
  distance: 132 - 140:  10.974
  distance: 134 - 135:  31.900
  distance: 135 - 136:  42.716
  distance: 135 - 137:   8.143
  distance: 136 - 138:   6.647
  distance: 137 - 139:  16.916
  distance: 138 - 139:  33.691
  distance: 140 - 141:  40.287
  distance: 142 - 143:  50.577
  distance: 142 - 145:  17.907
  distance: 145 - 146:  42.160
  distance: 146 - 147:  46.230
  distance: 146 - 149:   8.925
  distance: 147 - 148:   8.804
  distance: 147 - 150:  40.070
  distance: 152 - 158:  19.916
  distance: 154 - 155:  18.901
  distance: 155 - 156:  34.642
  distance: 155 - 157:   8.492
  distance: 158 - 159:  41.621
  distance: 158 - 164:  11.022
  distance: 159 - 160:  20.978
  distance: 159 - 162:  28.855
  distance: 160 - 165:  15.440
  distance: 162 - 163:  59.275
  distance: 165 - 166:  22.606
  distance: 166 - 167:  26.262
  distance: 166 - 169:  40.562
  distance: 167 - 168:   5.845
  distance: 170 - 176:  13.398
  distance: 171 - 172:  36.980
  distance: 171 - 174:  10.860
  distance: 172 - 173:  25.655
  distance: 172 - 177:  11.793