Starting phenix.real_space_refine
on Mon Jan 13 16:34:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jtt_36652/01_2025/8jtt_36652.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jtt_36652/01_2025/8jtt_36652.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/8jtt_36652/01_2025/8jtt_36652.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jtt_36652/01_2025/8jtt_36652.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jtt_36652/01_2025/8jtt_36652.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jtt_36652/01_2025/8jtt_36652.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=   0.001 sd=   0.083
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      21      5.16       5
     C    2182      2.51       5
     N     534      2.21       5
     O     584      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3321
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3312
          Classifications: {'peptide': 454}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 20, 'TRANS': 433}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 230
          Unresolved non-hydrogen angles: 277
          Unresolved non-hydrogen dihedrals: 197
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 113
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'MF8': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.84, per 1000 atoms: 0.86
  Number of scatterers: 3321
  At special positions: 0
  Unit cell: (85.5175, 58.455, 64.95, 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      21     16.00
     O     584      8.00
     N     534      7.00
     C    2182      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: 0.91
  Conformation dependent library (CDL) restraints added in 451.3 milliseconds
  

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  836

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      78.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 11
    Processing helix  chain 'A' and resid 15 through 30
    Processing helix  chain 'A' and resid 32 through 37
      removed outlier: 4.023A  pdb=" N   CYS A  36 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 42
    Processing helix  chain 'A' and resid 133 through 138
    Processing helix  chain 'A' and resid 143 through 173
      removed outlier: 3.515A  pdb=" N   LEU A 148 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ASP A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A 150 " --> pdb=" O   TRP A 146 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LEU A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ASP A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 195
      removed outlier: 3.724A  pdb=" N   PHE A 195 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 228
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 232 through 255
      removed outlier: 3.704A  pdb=" N   VAL A 236 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 278
      removed outlier: 3.907A  pdb=" N   LEU A 264 " --> pdb=" O   HIS A 260 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      Proline residue:  A 271  - end of helix
    Processing helix  chain 'A' and resid 285 through 291
    Processing helix  chain 'A' and resid 294 through 310
    Processing helix  chain 'A' and resid 320 through 324
      removed outlier: 3.794A  pdb=" N   GLU A 323 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 338
      removed outlier: 4.146A  pdb=" N   LEU A 337 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A 338 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 334 through 338'
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 5.596A  pdb=" N   LYS A 345 " --> pdb=" O   PRO A 341 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   ARG A 346 " --> pdb=" O   ARG A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 384
    Processing helix  chain 'A' and resid 385 through 397
      removed outlier: 3.749A  pdb=" N   GLY A 389 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 418
    Processing helix  chain 'A' and resid 419 through 422
    Processing helix  chain 'A' and resid 429 through 456
      removed outlier: 3.702A  pdb=" N   CYS A 450 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 470
    Processing helix  chain 'A' and resid 473 through 491
      Proline residue:  A 481  - end of helix
    Processing helix  chain 'A' and resid 492 through 510
      removed outlier: 3.962A  pdb=" N   LEU A 496 " --> pdb=" O   GLN A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 530
      removed outlier: 3.917A  pdb=" N   ALA A 528 " --> pdb=" O   THR A 524 " (cutoff:3.500A)

    236 hydrogen bonds defined for protein.
    696 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.93

  Time building geometry restraints manager: 1.05 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: 1031
        1.34 -     1.46: 712
        1.46 -     1.58: 1625
        1.58 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 3400
  Sorted by residual:
  bond pdb=" C07 MF8 A 601 "
       pdb=" N08 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.281  1.439 -0.158 2.00e-02 2.50e+03 6.28e+01
  bond pdb=" C07 MF8 A 601 "
       pdb=" N06 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.393  1.252  0.141 2.00e-02 2.50e+03 4.96e+01
  bond pdb=" C04 MF8 A 601 "
       pdb=" N02 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.362  1.448 -0.086 2.00e-02 2.50e+03 1.86e+01
  bond pdb=" C07 MF8 A 601 "
       pdb=" N09 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.358  1.444 -0.086 2.00e-02 2.50e+03 1.84e+01
  bond pdb=" C04 MF8 A 601 "
       pdb=" N06 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.454 -0.067 2.00e-02 2.50e+03 1.11e+01
  ... (remaining 3395 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 4470
        1.92 -     3.85: 157
        3.85 -     5.77: 19
        5.77 -     7.69: 12
        7.69 -     9.62: 3
  Bond angle restraints: 4661
  Sorted by residual:
  angle pdb=" N02 MF8 A 601 "
        pdb=" C04 MF8 A 601 "
        pdb=" N05 MF8 A 601 "
      ideal   model   delta    sigma   weight residual
     126.24  116.62    9.62 3.00e+00 1.11e-01 1.03e+01
  angle pdb=" N02 MF8 A 601 "
        pdb=" C04 MF8 A 601 "
        pdb=" N06 MF8 A 601 "
      ideal   model   delta    sigma   weight residual
     113.43  122.89   -9.46 3.00e+00 1.11e-01 9.93e+00
  angle pdb=" N   ARG A 439 "
        pdb=" CA  ARG A 439 "
        pdb=" C   ARG A 439 "
      ideal   model   delta    sigma   weight residual
     111.07  107.88    3.19 1.07e+00 8.73e-01 8.88e+00
  angle pdb=" N   MET A 448 "
        pdb=" CA  MET A 448 "
        pdb=" C   MET A 448 "
      ideal   model   delta    sigma   weight residual
     111.14  113.92   -2.78 1.08e+00 8.57e-01 6.62e+00
  angle pdb=" C   VAL A 212 "
        pdb=" CA  VAL A 212 "
        pdb=" CB  VAL A 212 "
      ideal   model   delta    sigma   weight residual
     112.22  108.70    3.52 1.38e+00 5.25e-01 6.52e+00
  ... (remaining 4656 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 1766
       16.55 -    33.10: 150
       33.10 -    49.65: 31
       49.65 -    66.20: 0
       66.20 -    82.75: 1
  Dihedral angle restraints: 1948
    sinusoidal: 648
      harmonic: 1300
  Sorted by residual:
  dihedral pdb=" CA  THR A 396 "
           pdb=" C   THR A 396 "
           pdb=" N   ILE A 397 "
           pdb=" CA  ILE A 397 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.54  -18.46     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  LEU A 521 "
           pdb=" C   LEU A 521 "
           pdb=" N   PRO A 522 "
           pdb=" CA  PRO A 522 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.07   15.93     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  LEU A  27 "
           pdb=" C   LEU A  27 "
           pdb=" N   LEU A  28 "
           pdb=" CA  LEU A  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.52   15.48     0      5.00e+00 4.00e-02 9.59e+00
  ... (remaining 1945 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 414
       0.048 -    0.097: 116
       0.097 -    0.145: 29
       0.145 -    0.193: 2
       0.193 -    0.241: 4
  Chirality restraints: 565
  Sorted by residual:
  chirality pdb=" CB  THR A  45 "
            pdb=" CA  THR A  45 "
            pdb=" OG1 THR A  45 "
            pdb=" CG2 THR A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CB  VAL A 228 "
            pdb=" CA  VAL A 228 "
            pdb=" CG1 VAL A 228 "
            pdb=" CG2 VAL A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL A 166 "
            pdb=" CA  VAL A 166 "
            pdb=" CG1 VAL A 166 "
            pdb=" CG2 VAL A 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 562 not shown)

  Planarity restraints: 581
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C01 MF8 A 601 "   -0.222 2.00e-02 2.50e+03   3.51e-01 2.78e+03
        pdb=" C03 MF8 A 601 "   -0.138 2.00e-02 2.50e+03
        pdb=" C04 MF8 A 601 "    0.229 2.00e-02 2.50e+03
        pdb=" C07 MF8 A 601 "   -0.097 2.00e-02 2.50e+03
        pdb=" N02 MF8 A 601 "   -0.043 2.00e-02 2.50e+03
        pdb=" N05 MF8 A 601 "    0.587 2.00e-02 2.50e+03
        pdb=" N06 MF8 A 601 "    0.083 2.00e-02 2.50e+03
        pdb=" N08 MF8 A 601 "    0.325 2.00e-02 2.50e+03
        pdb=" N09 MF8 A 601 "   -0.723 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 270 "   -0.039 5.00e-02 4.00e+02   5.85e-02 5.48e+00
        pdb=" N   PRO A 271 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 282 "   -0.032 5.00e-02 4.00e+02   4.86e-02 3.77e+00
        pdb=" N   PRO A 283 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 578 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 752
        2.78 -     3.31: 3285
        3.31 -     3.84: 5585
        3.84 -     4.37: 5758
        4.37 -     4.90: 9929
  Nonbonded interactions: 25309
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 409 "
            pdb=" O   GLY A 441 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   PHE A  22 "
            pdb=" OH  TYR A 240 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   LEU A  42 "
            pdb=" OG  SER A 133 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" OG1 THR A 245 "
            pdb=" OE1 GLU A 386 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" OG  SER A 189 "
            pdb=" OE1 GLN A 209 "
     model   vdw
     2.391 3.040
  ... (remaining 25304 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.100
  Find NCS groups from input model:        0.030
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5705
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      :  0.006   0.158   3400  Z= 0.400
  Angle     :  0.869   9.617   4661  Z= 0.444
  Chirality :  0.049   0.241    565
  Planarity :  0.016   0.351    581
  Dihedral  : 12.926  82.753   1112
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.35), residues: 450
  helix: -0.51 (0.26), residues: 327
  sheet:  None (None), residues: 0
  loop : -3.46 (0.45), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 217 
 HIS   0.002   0.001   HIS A 367 
 PHE   0.027   0.002   PHE A 482 
 TYR   0.015   0.001   TYR A 240 
 ARG   0.002   0.000   ARG A 234 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.358 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1038
  time to fit residues: 10.1013
Evaluate side-chains
  54 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.5401 r_free = 0.5401 target = 0.298009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5159 r_free = 0.5159 target = 0.267618 restraints weight = 3847.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.5204 r_free = 0.5204 target = 0.273793 restraints weight = 2234.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5226 r_free = 0.5226 target = 0.277489 restraints weight = 1522.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.5228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5834
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3400  Z= 0.190
  Angle     :  0.594  10.202   4661  Z= 0.304
  Chirality :  0.039   0.133    565
  Planarity :  0.005   0.049    581
  Dihedral  :  4.364  16.426    475
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  7.38 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.39), residues: 450
  helix:  0.35 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -3.13 (0.52), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.009   0.001   PHE A  22 
 TYR   0.010   0.001   TYR A 199 
 ARG   0.002   0.000   ARG A 262 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.317 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 60
  average time/residue: 0.0948
  time to fit residues: 8.0877
Evaluate side-chains
  58 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  354 TRP
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0370
   chunk 27 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 ASN ** 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 = 0.5515 r_free = 0.5515 target = 0.309205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.5262 r_free = 0.5262 target = 0.279598 restraints weight = 3734.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5305 r_free = 0.5305 target = 0.285580 restraints weight = 2227.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5324 r_free = 0.5324 target = 0.288848 restraints weight = 1550.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.5362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5856
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3400  Z= 0.166
  Angle     :  0.556   9.426   4661  Z= 0.281
  Chirality :  0.037   0.139    565
  Planarity :  0.004   0.046    581
  Dihedral  :  4.111  15.016    475
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.23 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.40), residues: 450
  helix:  0.69 (0.28), residues: 334
  sheet:  None (None), residues: 0
  loop : -3.11 (0.53), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A 260 
 PHE   0.009   0.001   PHE A 151 
 TYR   0.006   0.001   TYR A 352 
 ARG   0.002   0.000   ARG A 439 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.331 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0883
  time to fit residues: 7.4686
Evaluate side-chains
  60 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  354 TRP
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  442 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0070
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 24 optimal weight:    7.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 ASN ** 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 = 0.5494 r_free = 0.5494 target = 0.306604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5261 r_free = 0.5261 target = 0.278397 restraints weight = 3813.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.5289 r_free = 0.5289 target = 0.283835 restraints weight = 2258.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.5312 r_free = 0.5312 target = 0.287477 restraints weight = 1596.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.5336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5899
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3400  Z= 0.178
  Angle     :  0.554   9.160   4661  Z= 0.281
  Chirality :  0.037   0.135    565
  Planarity :  0.004   0.046    581
  Dihedral  :  4.073  14.968    475
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.31 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.40), residues: 450
  helix:  0.89 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -2.86 (0.53), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.024   0.001   PHE A 151 
 TYR   0.006   0.001   TYR A 240 
 ARG   0.002   0.000   ARG A 439 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.342 
Fit side-chains
  outliers start: 11
  outliers final: 6
  residues processed: 65
  average time/residue: 0.0964
  time to fit residues: 8.6938
Evaluate side-chains
  60 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  354 TRP
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  483 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   chunk 3 optimal weight:    0.2980
   chunk 25 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 410 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5399 r_free = 0.5399 target = 0.296836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5171 r_free = 0.5171 target = 0.269067 restraints weight = 3931.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5210 r_free = 0.5210 target = 0.274551 restraints weight = 2371.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5228 r_free = 0.5228 target = 0.277765 restraints weight = 1661.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.5248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5954
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3400  Z= 0.192
  Angle     :  0.565   8.997   4661  Z= 0.288
  Chirality :  0.038   0.134    565
  Planarity :  0.004   0.045    581
  Dihedral  :  4.069  15.126    475
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.77 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.41), residues: 450
  helix:  0.91 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -2.77 (0.54), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.010   0.001   PHE A 151 
 TYR   0.006   0.001   TYR A 240 
 ARG   0.002   0.000   ARG A 439 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.345 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 62
  average time/residue: 0.0911
  time to fit residues: 7.9621
Evaluate side-chains
  63 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  354 TRP
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  483 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0770
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 ASN ** 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 = 0.5463 r_free = 0.5463 target = 0.302334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5212 r_free = 0.5212 target = 0.273281 restraints weight = 3870.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.5253 r_free = 0.5253 target = 0.278936 restraints weight = 2338.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.5272 r_free = 0.5272 target = 0.282187 restraints weight = 1624.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.5328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6004
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3400  Z= 0.201
  Angle     :  0.596   8.947   4661  Z= 0.299
  Chirality :  0.038   0.136    565
  Planarity :  0.004   0.045    581
  Dihedral  :  4.121  15.291    475
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.92 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.41), residues: 450
  helix:  0.84 (0.29), residues: 329
  sheet:  None (None), residues: 0
  loop : -2.76 (0.56), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 261 
 HIS   0.004   0.001   HIS A 260 
 PHE   0.026   0.002   PHE A 151 
 TYR   0.008   0.001   TYR A 240 
 ARG   0.002   0.000   ARG A 439 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.324 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 62
  average time/residue: 0.0904
  time to fit residues: 7.7768
Evaluate side-chains
  62 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  354 TRP
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  442 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0270
   chunk 41 optimal weight:    0.0770
   chunk 15 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 ASN ** 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 = 0.5473 r_free = 0.5473 target = 0.304135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5233 r_free = 0.5233 target = 0.276043 restraints weight = 3796.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.5275 r_free = 0.5275 target = 0.281769 restraints weight = 2284.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5293 r_free = 0.5293 target = 0.284970 restraints weight = 1571.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.5236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5904
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3400  Z= 0.174
  Angle     :  0.574   8.964   4661  Z= 0.286
  Chirality :  0.037   0.128    565
  Planarity :  0.004   0.046    581
  Dihedral  :  3.996  15.446    475
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.54 %
    Favored  : 75.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.41), residues: 450
  helix:  0.97 (0.29), residues: 329
  sheet:  None (None), residues: 0
  loop : -2.74 (0.55), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A 260 
 PHE   0.009   0.001   PHE A 151 
 TYR   0.005   0.001   TYR A 199 
 ARG   0.002   0.000   ARG A 175 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  173 PHE cc_start: 0.4574 (OUTLIER) cc_final: 0.4081 (m-10)
  outliers start: 10
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0967
  time to fit residues: 8.6996
Evaluate side-chains
  65 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  354 TRP
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  442 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 ASN ** 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 = 0.5457 r_free = 0.5457 target = 0.302008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5219 r_free = 0.5219 target = 0.274283 restraints weight = 3810.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5251 r_free = 0.5251 target = 0.279710 restraints weight = 2219.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5291 r_free = 0.5291 target = 0.283821 restraints weight = 1530.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.5295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6011
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3400  Z= 0.222
  Angle     :  0.609   8.771   4661  Z= 0.310
  Chirality :  0.039   0.141    565
  Planarity :  0.004   0.046    581
  Dihedral  :  4.114  15.354    475
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.15 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.41), residues: 450
  helix:  0.81 (0.29), residues: 329
  sheet:  None (None), residues: 0
  loop : -2.70 (0.56), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A 260 
 PHE   0.014   0.001   PHE A 499 
 TYR   0.006   0.001   TYR A 240 
 ARG   0.003   0.000   ARG A 206 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  173 PHE cc_start: 0.4821 (OUTLIER) cc_final: 0.4356 (m-10)
REVERT: A  260 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.7001 (t-90)
  outliers start: 11
  outliers final: 8
  residues processed: 62
  average time/residue: 0.0929
  time to fit residues: 8.1903
Evaluate side-chains
  64 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  260 HIS
Chi-restraints excluded: chain A residue  354 TRP
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  442 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 52.5217 > 50:
  distance: 22 - 38:   4.241
  distance: 26 - 43:   3.205
  distance: 30 - 51:  10.997
  distance: 34 - 56:  14.658
  distance: 38 - 39:   3.940
  distance: 39 - 40:   4.615
  distance: 39 - 42:  12.241
  distance: 40 - 41:   3.205
  distance: 40 - 43:   5.436
  distance: 41 - 64:  29.462
  distance: 43 - 44:   7.913
  distance: 44 - 45:   5.037
  distance: 44 - 47:   8.382
  distance: 45 - 46:   7.182
  distance: 45 - 51:   4.739
  distance: 46 - 72:  22.203
  distance: 47 - 48:   6.569
  distance: 47 - 49:  10.308
  distance: 48 - 50:  12.125
  distance: 51 - 52:   6.670
  distance: 52 - 53:   4.511
  distance: 52 - 55:   4.443
  distance: 53 - 56:   4.680
  distance: 54 - 80:  17.006
  distance: 56 - 57:   8.471
  distance: 57 - 58:  11.972
  distance: 57 - 60:  13.100
  distance: 58 - 59:   7.833
  distance: 58 - 64:  28.702
  distance: 59 - 90:  12.623
  distance: 60 - 61:  18.425
  distance: 60 - 62:  19.038
  distance: 61 - 63:   9.544
  distance: 64 - 65:  35.722
  distance: 65 - 66:   3.432
  distance: 65 - 68:  18.181
  distance: 66 - 67:   4.562
  distance: 67 - 98:  14.605
  distance: 68 - 69:  28.505
  distance: 69 - 70:  39.718
  distance: 70 - 71:  26.256
  distance: 72 - 73:   9.737
  distance: 73 - 74:   8.699
  distance: 73 - 76:   7.907
  distance: 74 - 75:   8.056
  distance: 74 - 80:   3.988
  distance: 75 - 103:   6.684
  distance: 76 - 77:   7.904
  distance: 77 - 78:   6.393
  distance: 77 - 79:   5.501
  distance: 81 - 82:   3.027
  distance: 82 - 83:   4.753
  distance: 82 - 90:   3.931
  distance: 83 - 108:   3.545
  distance: 84 - 85:   3.783
  distance: 85 - 86:   3.800
  distance: 85 - 87:   5.668
  distance: 86 - 88:   3.320
  distance: 88 - 89:   5.349
  distance: 90 - 91:   3.566
  distance: 91 - 92:   4.226
  distance: 91 - 94:   6.663
  distance: 92 - 93:   5.294
  distance: 92 - 98:   6.476
  distance: 93 - 113:  11.883
  distance: 94 - 95:   4.624
  distance: 94 - 96:   8.319
  distance: 95 - 97:   6.916
  distance: 98 - 99:   3.796
  distance: 99 - 102:   4.144
  distance: 100 - 101:   4.831
  distance: 101 - 121:  14.777
  distance: 104 - 105:   6.264
  distance: 105 - 108:   3.700