Starting phenix.real_space_refine
on Tue Feb 11 19:04:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b7q_15899/02_2025/8b7q_15899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b7q_15899/02_2025/8b7q_15899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b7q_15899/02_2025/8b7q_15899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b7q_15899/02_2025/8b7q_15899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b7q_15899/02_2025/8b7q_15899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b7q_15899/02_2025/8b7q_15899.cif"
  }
  resolution = 4.02
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3495 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2236      2.51       5
     N     594      2.21       5
     O     663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3511
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1064
          Classifications: {'peptide': 138}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 131}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1637
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 190}
    Chain: "F"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 796
          Classifications: {'peptide': 97}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.10, per 1000 atoms: 1.17
  Number of scatterers: 3511
  At special positions: 0
  Unit cell: (79.584, 98.651, 88.703, 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      18     16.00
     O     663      8.00
     N     594      7.00
     C    2236      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 411 " - pdb=" SG  CYS F 416 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG F 901 " - " ASN F 345 "
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 380.1 milliseconds
  

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  850

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      25.9% alpha, 32.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 45
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.870A  pdb=" N   GLN A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   SER A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 50'
    Processing helix  chain 'A' and resid 71 through 89
      removed outlier: 3.647A  pdb=" N   SER A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 113
    Processing helix  chain 'A' and resid 130 through 138
    Processing helix  chain 'A' and resid 138 through 162
      removed outlier: 4.117A  pdb=" N   ASP A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.963A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 375 through 377
      No H-bonds generated for 'chain 'F' and resid 375 through 377'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 432 through 436
      removed outlier: 3.536A  pdb=" N   TRP B 447 " --> pdb=" O   TYR B 494 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 539 through 546
      removed outlier: 5.035A  pdb=" N   ASN B 540 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLU B 557 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 582 through 586
    Processing sheet with id=AA6, first strand: chain 'F' and resid 331 through 334
    Processing sheet with id=AA7, first strand: chain 'F' and resid 331 through 334
      removed outlier: 3.552A  pdb=" N   ALA F 346 " --> pdb=" O   PHE F 391 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 337 through 340
      removed outlier: 7.582A  pdb=" N   HIS F 417 " --> pdb=" O   ASN F 412 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   ASN F 412 " --> pdb=" O   HIS F 417 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ARG F 419 " --> pdb=" O   CYS F 410 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   CYS F 410 " --> pdb=" O   ARG F 419 " (cutoff:3.500A)

    175 hydrogen bonds defined for protein.
    474 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: 0.94

  Time building geometry restraints manager: 0.86 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: 1124
        1.34 -     1.46: 812
        1.46 -     1.58: 1630
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 3588
  Sorted by residual:
  bond pdb=" C1  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C5  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  bond pdb=" C3  NAG F 901 "
       pdb=" O3  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.76e-01
  bond pdb=" C   TRP B 447 "
       pdb=" N   SER B 448 "
    ideal  model  delta    sigma   weight residual
    1.332  1.347 -0.015 1.92e-02 2.71e+03 6.28e-01
  bond pdb=" N   SER A 114 "
       pdb=" CA  SER A 114 "
    ideal  model  delta    sigma   weight residual
    1.463  1.455  0.008 1.08e-02 8.57e+03 5.33e-01
  ... (remaining 3583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 4692
        1.40 -     2.81: 165
        2.81 -     4.21: 26
        4.21 -     5.62: 1
        5.62 -     7.02: 1
  Bond angle restraints: 4885
  Sorted by residual:
  angle pdb=" C   ILE A  63 "
        pdb=" N   PRO A  64 "
        pdb=" CA  PRO A  64 "
      ideal   model   delta    sigma   weight residual
     119.84  122.92   -3.08 1.25e+00 6.40e-01 6.05e+00
  angle pdb=" C   PHE A 113 "
        pdb=" N   SER A 114 "
        pdb=" CA  SER A 114 "
      ideal   model   delta    sigma   weight residual
     120.89  124.35   -3.46 1.50e+00 4.44e-01 5.32e+00
  angle pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
        pdb=" C   SER A  46 "
      ideal   model   delta    sigma   weight residual
     111.37  115.17   -3.80 1.65e+00 3.67e-01 5.30e+00
  angle pdb=" C   ILE A  45 "
        pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
      ideal   model   delta    sigma   weight residual
     120.82  124.00   -3.18 1.50e+00 4.44e-01 4.50e+00
  angle pdb=" N   LEU B 503 "
        pdb=" CA  LEU B 503 "
        pdb=" C   LEU B 503 "
      ideal   model   delta    sigma   weight residual
     111.33  113.75   -2.42 1.21e+00 6.83e-01 4.01e+00
  ... (remaining 4880 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 2086
       15.92 -    31.83: 94
       31.83 -    47.75: 22
       47.75 -    63.66: 4
       63.66 -    79.58: 2
  Dihedral angle restraints: 2208
    sinusoidal: 903
      harmonic: 1305
  Sorted by residual:
  dihedral pdb=" CB  CYS F 350 "
           pdb=" SG  CYS F 350 "
           pdb=" SG  CYS F 410 "
           pdb=" CB  CYS F 410 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.39   29.61     1      1.00e+01 1.00e-02 1.25e+01
  dihedral pdb=" N   LEU A 161 "
           pdb=" CA  LEU A 161 "
           pdb=" CB  LEU A 161 "
           pdb=" CG  LEU A 161 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.82  -58.18     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   PHE F 334 "
           pdb=" CA  PHE F 334 "
           pdb=" CB  PHE F 334 "
           pdb=" CG  PHE F 334 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.09   51.09     3      1.50e+01 4.44e-03 8.98e+00
  ... (remaining 2205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 349
       0.031 -    0.062: 154
       0.062 -    0.092: 33
       0.092 -    0.123: 31
       0.123 -    0.154: 5
  Chirality restraints: 572
  Sorted by residual:
  chirality pdb=" CA  ILE F 351 "
            pdb=" N   ILE F 351 "
            pdb=" C   ILE F 351 "
            pdb=" CB  ILE F 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.91e-01
  chirality pdb=" CA  PRO A  64 "
            pdb=" N   PRO A  64 "
            pdb=" C   PRO A  64 "
            pdb=" CB  PRO A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  ILE F 374 "
            pdb=" N   ILE F 374 "
            pdb=" C   ILE F 374 "
            pdb=" CB  ILE F 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 569 not shown)

  Planarity restraints: 616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 155 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   GLN A 155 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLN A 155 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP A 156 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 448 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO B 449 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 148 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" C   SER A 148 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   SER A 148 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ARG A 149 "    0.007 2.00e-02 2.50e+03
  ... (remaining 613 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 532
        2.77 -     3.30: 3250
        3.30 -     3.83: 5553
        3.83 -     4.37: 6419
        4.37 -     4.90: 11088
  Nonbonded interactions: 26842
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 141 "
            pdb=" OH  TYR F 409 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   PRO A  64 "
            pdb=" OH  TYR A  82 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD2 ASP A  30 "
            pdb=" OH  TYR B 470 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NH2 ARG B 571 "
            pdb=" OE1 GLN B 608 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" NH2 ARG F 400 "
            pdb=" O   TYR F 405 "
     model   vdw
     2.378 3.120
  ... (remaining 26837 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.080
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3588  Z= 0.173
  Angle     :  0.599   7.021   4885  Z= 0.335
  Chirality :  0.043   0.154    572
  Planarity :  0.004   0.035    615
  Dihedral  :  9.873  79.577   1340
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  3.93 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  6.13 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  0.29 (0.38), residues: 433
  helix:  0.92 (0.47), residues: 97
  sheet:  0.83 (0.39), residues: 134
  loop : -0.57 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 367 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.010   0.001   PHE B 493 
 TYR   0.009   0.001   TYR F 424 
 ARG   0.002   0.000   ARG B 467 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ILE cc_start: 0.7042 (mt) cc_final: 0.6621 (mm)
REVERT: A   63 ILE cc_start: 0.8987 (mt) cc_final: 0.8664 (tt)
REVERT: A   93 ASN cc_start: 0.7569 (m-40) cc_final: 0.7287 (m-40)
REVERT: B  436 THR cc_start: 0.9047 (m) cc_final: 0.8331 (m)
REVERT: B  540 ASN cc_start: 0.8477 (t0) cc_final: 0.8226 (t0)
REVERT: B  565 ASN cc_start: 0.8276 (m-40) cc_final: 0.7795 (p0)
REVERT: B  572 TYR cc_start: 0.8019 (p90) cc_final: 0.7631 (p90)
REVERT: B  585 GLU cc_start: 0.8506 (mp0) cc_final: 0.8236 (pm20)
REVERT: B  609 VAL cc_start: 0.9427 (t) cc_final: 0.9200 (m)
REVERT: B  612 ARG cc_start: 0.8665 (ttt180) cc_final: 0.7832 (ttt-90)
REVERT: F  365 VAL cc_start: 0.8987 (m) cc_final: 0.8090 (p)
REVERT: F  388 LYS cc_start: 0.8796 (tttt) cc_final: 0.8555 (tttp)
REVERT: F  393 ASN cc_start: 0.7524 (t0) cc_final: 0.7077 (t0)
  outliers start: 12
  outliers final: 2
  residues processed: 155
  average time/residue: 0.1680
  time to fit residues: 31.2309
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.113202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.092823 restraints weight = 8006.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.095592 restraints weight = 4680.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.097557 restraints weight = 3230.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3588  Z= 0.217
  Angle     :  0.631  10.846   4885  Z= 0.322
  Chirality :  0.046   0.266    572
  Planarity :  0.004   0.042    615
  Dihedral  :  4.335  16.588    496
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  1.72 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  1.14 (0.40), residues: 433
  helix:  2.30 (0.50), residues: 103
  sheet:  0.55 (0.38), residues: 135
  loop :  0.16 (0.48), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 620 
 HIS   0.003   0.001   HIS F 418 
 PHE   0.012   0.002   PHE A 113 
 TYR   0.020   0.002   TYR A  82 
 ARG   0.004   0.000   ARG F 419 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8096 (ttpt)
REVERT: A   93 ASN cc_start: 0.7648 (m-40) cc_final: 0.7427 (m-40)
REVERT: B  572 TYR cc_start: 0.8108 (p90) cc_final: 0.7725 (p90)
REVERT: B  609 VAL cc_start: 0.9487 (t) cc_final: 0.9281 (m)
REVERT: B  612 ARG cc_start: 0.8862 (ttt180) cc_final: 0.8333 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8682 (pt) cc_final: 0.8463 (mm)
REVERT: F  393 ASN cc_start: 0.7583 (t0) cc_final: 0.6997 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1467
  time to fit residues: 20.5546
Evaluate side-chains
  89 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    0.4980
   chunk 18 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 GLN
B 461 GLN
B 499 GLN
F 354 ASN
F 369 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.111964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.091295 restraints weight = 8052.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.093920 restraints weight = 4865.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.095754 restraints weight = 3417.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3588  Z= 0.227
  Angle     :  0.620  14.067   4885  Z= 0.318
  Chirality :  0.046   0.230    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.442  25.778    496
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.94 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  1.37 (0.41), residues: 433
  helix:  2.67 (0.50), residues: 102
  sheet:  0.67 (0.42), residues: 123
  loop :  0.26 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.011   0.001   PHE F 348 
 TYR   0.016   0.001   TYR F 352 
 ARG   0.002   0.000   ARG F 368 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8306 (ttpt)
REVERT: B  429 ASN cc_start: 0.8917 (t0) cc_final: 0.8627 (t0)
REVERT: B  437 ASP cc_start: 0.8935 (p0) cc_final: 0.8735 (p0)
REVERT: B  609 VAL cc_start: 0.9442 (t) cc_final: 0.9201 (m)
REVERT: B  612 ARG cc_start: 0.8876 (ttt180) cc_final: 0.8474 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8640 (pt) cc_final: 0.8353 (mm)
REVERT: F  393 ASN cc_start: 0.7512 (t0) cc_final: 0.6942 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1470
  time to fit residues: 19.0957
Evaluate side-chains
  87 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.112061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.091429 restraints weight = 8028.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.094036 restraints weight = 4908.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.095837 restraints weight = 3490.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3588  Z= 0.198
  Angle     :  0.594  11.563   4885  Z= 0.302
  Chirality :  0.045   0.196    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.363  24.246    496
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.72 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  1.43 (0.41), residues: 433
  helix:  2.78 (0.50), residues: 102
  sheet:  0.72 (0.42), residues: 130
  loop :  0.22 (0.47), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.009   0.001   PHE F 348 
 TYR   0.019   0.002   TYR B 572 
 ARG   0.002   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8195 (ptm-80)
REVERT: A   69 ILE cc_start: 0.7213 (tp) cc_final: 0.6981 (tp)
REVERT: A   74 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8261 (ttpt)
REVERT: B  429 ASN cc_start: 0.8906 (t0) cc_final: 0.8619 (t0)
REVERT: B  572 TYR cc_start: 0.8003 (p90) cc_final: 0.7714 (p90)
REVERT: B  609 VAL cc_start: 0.9463 (t) cc_final: 0.9213 (m)
REVERT: B  612 ARG cc_start: 0.8882 (ttt180) cc_final: 0.8461 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8648 (pt) cc_final: 0.8270 (mm)
REVERT: F  393 ASN cc_start: 0.7498 (t0) cc_final: 0.6849 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1497
  time to fit residues: 18.9921
Evaluate side-chains
  82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.110937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.090498 restraints weight = 8255.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.093109 restraints weight = 5019.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.094915 restraints weight = 3543.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.4604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3588  Z= 0.209
  Angle     :  0.600  11.872   4885  Z= 0.306
  Chirality :  0.045   0.189    572
  Planarity :  0.004   0.029    615
  Dihedral  :  4.559  32.424    496
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.52 (0.41), residues: 433
  helix:  3.31 (0.51), residues: 96
  sheet:  0.78 (0.42), residues: 128
  loop :  0.11 (0.46), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.009   0.001   PHE F 334 
 TYR   0.014   0.001   TYR B 572 
 ARG   0.004   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8201 (ptm160)
REVERT: A   69 ILE cc_start: 0.7120 (tp) cc_final: 0.6877 (tp)
REVERT: A   74 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8299 (ttpt)
REVERT: B  429 ASN cc_start: 0.8874 (t0) cc_final: 0.8614 (t0)
REVERT: B  453 GLN cc_start: 0.8709 (pt0) cc_final: 0.8305 (pm20)
REVERT: B  542 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8296 (mmtm)
REVERT: B  612 ARG cc_start: 0.8868 (ttt180) cc_final: 0.8492 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8644 (pt) cc_final: 0.8358 (mm)
REVERT: F  393 ASN cc_start: 0.7441 (t0) cc_final: 0.6902 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1533
  time to fit residues: 17.8466
Evaluate side-chains
  82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
F 354 ASN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.109519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.088566 restraints weight = 8401.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.091166 restraints weight = 5189.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.093012 restraints weight = 3682.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3588  Z= 0.226
  Angle     :  0.599  10.221   4885  Z= 0.307
  Chirality :  0.045   0.187    572
  Planarity :  0.004   0.027    615
  Dihedral  :  4.595  33.204    496
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.41), residues: 433
  helix:  2.75 (0.50), residues: 102
  sheet:  0.77 (0.42), residues: 128
  loop : -0.03 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 623 
 HIS   0.004   0.001   HIS B 465 
 PHE   0.011   0.001   PHE F 334 
 TYR   0.012   0.001   TYR F 424 
 ARG   0.004   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8180 (ptm160)
REVERT: A   69 ILE cc_start: 0.7147 (tp) cc_final: 0.6725 (tp)
REVERT: A   74 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8317 (ttpt)
REVERT: B  429 ASN cc_start: 0.8855 (t0) cc_final: 0.8603 (t0)
REVERT: B  453 GLN cc_start: 0.8750 (pt0) cc_final: 0.8185 (pm20)
REVERT: B  542 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8276 (mmtm)
REVERT: B  572 TYR cc_start: 0.8016 (p90) cc_final: 0.7629 (p90)
REVERT: B  612 ARG cc_start: 0.8906 (ttt180) cc_final: 0.8481 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7476 (t0) cc_final: 0.6743 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1480
  time to fit residues: 17.8641
Evaluate side-chains
  79 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0020
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 453 GLN
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.112287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.091931 restraints weight = 8085.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.094551 restraints weight = 4908.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.096264 restraints weight = 3458.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.5061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3588  Z= 0.178
  Angle     :  0.580   9.212   4885  Z= 0.294
  Chirality :  0.044   0.171    572
  Planarity :  0.003   0.027    615
  Dihedral  :  4.447  30.432    496
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.36 (0.41), residues: 433
  helix:  2.55 (0.51), residues: 108
  sheet:  0.95 (0.43), residues: 127
  loop : -0.01 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.008   0.001   PHE F 334 
 TYR   0.010   0.001   TYR A  82 
 ARG   0.003   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8198 (ptm160)
REVERT: A   69 ILE cc_start: 0.7089 (tp) cc_final: 0.6624 (tp)
REVERT: A   74 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8276 (ttpt)
REVERT: B  429 ASN cc_start: 0.8828 (t0) cc_final: 0.8575 (t0)
REVERT: B  453 GLN cc_start: 0.8650 (pt0) cc_final: 0.8115 (pm20)
REVERT: B  542 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8291 (mmtm)
REVERT: B  572 TYR cc_start: 0.8003 (p90) cc_final: 0.7608 (p90)
REVERT: B  612 ARG cc_start: 0.8890 (ttt180) cc_final: 0.8506 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7489 (t0) cc_final: 0.6888 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1497
  time to fit residues: 17.9249
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0770
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.112890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.092487 restraints weight = 8131.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.095098 restraints weight = 4894.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.096933 restraints weight = 3439.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.5178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3588  Z= 0.164
  Angle     :  0.570   8.306   4885  Z= 0.289
  Chirality :  0.045   0.173    572
  Planarity :  0.003   0.027    615
  Dihedral  :  4.429  34.482    496
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.44 (0.41), residues: 433
  helix:  2.57 (0.52), residues: 108
  sheet:  1.07 (0.44), residues: 125
  loop :  0.02 (0.46), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 584 
 PHE   0.009   0.001   PHE F 334 
 TYR   0.009   0.001   TYR F 424 
 ARG   0.001   0.000   ARG B 613 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8199 (ptm160)
REVERT: B  429 ASN cc_start: 0.8816 (t0) cc_final: 0.8616 (t0)
REVERT: B  542 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8303 (mmtm)
REVERT: B  612 ARG cc_start: 0.8898 (ttt180) cc_final: 0.8548 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7497 (t0) cc_final: 0.6882 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1631
  time to fit residues: 18.6578
Evaluate side-chains
  78 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0970
   chunk 3 optimal weight:    0.2980
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 453 GLN
B 485 ASN
B 499 GLN
F 369 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.110389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.090320 restraints weight = 8080.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.092723 restraints weight = 5014.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.094444 restraints weight = 3593.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.5285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3588  Z= 0.237
  Angle     :  0.631   8.409   4885  Z= 0.324
  Chirality :  0.046   0.223    572
  Planarity :  0.004   0.029    615
  Dihedral  :  4.675  37.547    496
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.98 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.42 (0.41), residues: 433
  helix:  2.68 (0.52), residues: 102
  sheet:  0.87 (0.42), residues: 139
  loop :  0.10 (0.48), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 620 
 HIS   0.004   0.001   HIS B 465 
 PHE   0.012   0.001   PHE F 334 
 TYR   0.019   0.001   TYR A  82 
 ARG   0.001   0.000   ARG F 385 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8229 (ptm160)
REVERT: A   74 LYS cc_start: 0.8660 (ttpt) cc_final: 0.8407 (ttpt)
REVERT: B  429 ASN cc_start: 0.8841 (t0) cc_final: 0.8415 (t0)
REVERT: B  453 GLN cc_start: 0.8741 (pt0) cc_final: 0.8211 (pm20)
REVERT: B  612 ARG cc_start: 0.8875 (ttt180) cc_final: 0.8427 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7336 (t0) cc_final: 0.6567 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1619
  time to fit residues: 19.4169
Evaluate side-chains
  79 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 58.7565 > 50:
  distance: 21 - 42:   5.239
  distance: 25 - 50:   6.743
  distance: 30 - 55:  36.778
  distance: 42 - 43:   3.274
  distance: 43 - 44:   7.522
  distance: 43 - 46:   8.418
  distance: 44 - 45:   7.868
  distance: 44 - 50:   6.989
  distance: 46 - 47:   8.359
  distance: 47 - 48:  10.782
  distance: 47 - 49:   8.270
  distance: 50 - 51:  13.494
  distance: 51 - 52:  38.178
  distance: 51 - 54:  12.218
  distance: 52 - 53:  17.164
  distance: 52 - 55:  58.757
  distance: 55 - 56:  57.054
  distance: 56 - 57:  41.516
  distance: 56 - 59:  26.416
  distance: 57 - 58:  13.942
  distance: 57 - 66:  13.025
  distance: 59 - 60:   8.932
  distance: 60 - 61:  14.923
  distance: 60 - 62:   8.310
  distance: 61 - 63:   6.542
  distance: 62 - 64:   8.785
  distance: 63 - 65:   8.992
  distance: 64 - 65:  13.730
  distance: 66 - 67:   4.721
  distance: 67 - 68:   6.078
  distance: 67 - 70:   3.248
  distance: 68 - 69:   7.727
  distance: 68 - 72:   5.851
  distance: 72 - 73:   8.668
  distance: 73 - 74:  10.188
  distance: 74 - 75:   8.387
  distance: 74 - 81:   3.236
  distance: 76 - 77:   7.476
  distance: 77 - 78:   6.435
  distance: 78 - 79:   7.179
  distance: 79 - 80:  11.395
  distance: 81 - 82:   5.924
  distance: 82 - 83:   6.168
  distance: 82 - 85:   6.802
  distance: 83 - 84:  10.134
  distance: 83 - 87:   7.269
  distance: 85 - 86:   6.317
  distance: 87 - 88:   4.024
  distance: 88 - 89:  11.400
  distance: 88 - 91:   3.605
  distance: 89 - 90:   8.644
  distance: 89 - 93:   7.057
  distance: 91 - 92:   7.669
  distance: 92 - 122:   5.885
  distance: 93 - 94:   8.466
  distance: 94 - 95:   3.991
  distance: 95 - 96:  12.925
  distance: 95 - 99:   6.298
  distance: 97 - 98:   6.327
  distance: 99 - 100:   7.184
  distance: 100 - 101:   8.656
  distance: 100 - 103:  12.750
  distance: 101 - 102:   3.302
  distance: 101 - 107:  10.104
  distance: 103 - 104:   7.982
  distance: 104 - 105:  15.831
  distance: 104 - 106:   8.230
  distance: 107 - 108:   8.934
  distance: 107 - 113:   9.275
  distance: 108 - 109:   5.485
  distance: 108 - 111:   9.071
  distance: 109 - 110:  16.417
  distance: 111 - 112:   6.764
  distance: 112 - 113:   9.007