Starting phenix.real_space_refine
on Fri Aug 22 13:34:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wed_32447/08_2025/7wed_32447.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wed_32447/08_2025/7wed_32447.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wed_32447/08_2025/7wed_32447.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wed_32447/08_2025/7wed_32447.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wed_32447/08_2025/7wed_32447.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wed_32447/08_2025/7wed_32447.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2132      2.51       5
     N     572      2.21       5
     O     638      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3358
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 1610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1610
          Classifications: {'peptide': 201}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187}
    Chain: "H"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 941
          Classifications: {'peptide': 123}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "L"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 807
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 0.89, per 1000 atoms: 0.27
  Number of scatterers: 3358
  At special positions: 0
  Unit cell: (110.21, 72.76, 72.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     638      8.00
     N     572      7.00
     C    2132      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 102 " - pdb=" SG  CYS H 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.04

  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: 0.22
  Conformation dependent library (CDL) restraints added in 81.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  798

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 8 sheets defined
      8.4% alpha, 31.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'E' and resid 337 through 343
    Processing helix  chain 'E' and resid 365 through 370
      removed outlier: 3.570A  pdb=" N   ASN E 370 " --> pdb=" O   SER E 366 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 385 through 390
      removed outlier: 4.403A  pdb=" N   ASN E 388 " --> pdb=" O   THR E 385 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASP E 389 " --> pdb=" O   LYS E 386 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 405 through 411
      removed outlier: 4.400A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA E 411 " --> pdb=" O   ARG E 408 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 416 through 421
    Processing helix  chain 'H' and resid 63 through 66
      removed outlier: 3.749A  pdb=" N   GLN H  66 " --> pdb=" O   PRO H  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 63 through 66'
    Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358
      removed outlier: 4.234A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLU E 516 " --> pdb=" O   ASN E 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.789A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.620A  pdb=" N   THR H 118 " --> pdb=" O   TYR H  95 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU H  35 " --> pdb=" O   TRP H  51 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   TRP H  51 " --> pdb=" O   LEU H  35 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   TRP H  37 " --> pdb=" O   ILE H  49 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TRP H  51 " --> pdb=" O   ASN H  60 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.620A  pdb=" N   THR H 118 " --> pdb=" O   TYR H  95 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.284A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   THR L 103 " --> pdb=" O   TYR L  87 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   VAL L  86 " --> pdb=" O   GLN L  39 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE L  49 " --> pdb=" O   TRP L  36 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER L  54 " --> pdb=" O   SER L  50 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    243 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: 0.28

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1076
        1.35 -     1.47: 922
        1.47 -     1.59: 1429
        1.59 -     1.71: 0
        1.71 -     1.83: 18
  Bond restraints: 3445
  Sorted by residual:
  bond pdb=" C   SER L  95 "
       pdb=" N   PRO L  96 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 3.99e+00
  bond pdb=" C   CYS E 432 "
       pdb=" N   VAL E 433 "
    ideal  model  delta    sigma   weight residual
    1.331  1.348 -0.017 1.50e-02 4.44e+03 1.33e+00
  bond pdb=" CB  ARG H  42 "
       pdb=" CG  ARG H  42 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.25e+00
  bond pdb=" C   ASN E 331 "
       pdb=" N   ILE E 332 "
    ideal  model  delta    sigma   weight residual
    1.329  1.344 -0.015 1.40e-02 5.10e+03 1.19e+00
  bond pdb=" CB  ARG L  18 "
       pdb=" CG  ARG L  18 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.21e-01
  ... (remaining 3440 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 4515
        1.65 -     3.30: 136
        3.30 -     4.95: 31
        4.95 -     6.60: 2
        6.60 -     8.25: 2
  Bond angle restraints: 4686
  Sorted by residual:
  angle pdb=" C   ASN E 331 "
        pdb=" N   ILE E 332 "
        pdb=" CA  ILE E 332 "
      ideal   model   delta    sigma   weight residual
     121.70  129.09   -7.39 1.80e+00 3.09e-01 1.68e+01
  angle pdb=" CA  CYS E 432 "
        pdb=" CB  CYS E 432 "
        pdb=" SG  CYS E 432 "
      ideal   model   delta    sigma   weight residual
     114.40  122.65   -8.25 2.30e+00 1.89e-01 1.29e+01
  angle pdb=" C   LYS E 378 "
        pdb=" N   CYS E 379 "
        pdb=" CA  CYS E 379 "
      ideal   model   delta    sigma   weight residual
     122.73  117.86    4.87 1.62e+00 3.81e-01 9.02e+00
  angle pdb=" CA  ASN E 331 "
        pdb=" C   ASN E 331 "
        pdb=" N   ILE E 332 "
      ideal   model   delta    sigma   weight residual
     117.07  120.32   -3.25 1.21e+00 6.83e-01 7.22e+00
  angle pdb=" C   ASN L  94 "
        pdb=" N   SER L  95 "
        pdb=" CA  SER L  95 "
      ideal   model   delta    sigma   weight residual
     121.80  128.12   -6.32 2.44e+00 1.68e-01 6.72e+00
  ... (remaining 4681 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 1822
       17.59 -    35.17: 191
       35.17 -    52.76: 28
       52.76 -    70.34: 2
       70.34 -    87.93: 3
  Dihedral angle restraints: 2046
    sinusoidal: 796
      harmonic: 1250
  Sorted by residual:
  dihedral pdb=" CA  SER H 103 "
           pdb=" C   SER H 103 "
           pdb=" N   GLU H 104 "
           pdb=" CA  GLU H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.40   29.60     0      5.00e+00 4.00e-02 3.51e+01
  dihedral pdb=" CB  CYS E 480 "
           pdb=" SG  CYS E 480 "
           pdb=" SG  CYS E 488 "
           pdb=" CB  CYS E 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.50  -48.50     1      1.00e+01 1.00e-02 3.24e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  97 "
           pdb=" CB  CYS H  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  135.33  -42.33     1      1.00e+01 1.00e-02 2.50e+01
  ... (remaining 2043 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 298
       0.032 -    0.063: 135
       0.063 -    0.094: 42
       0.094 -    0.126: 29
       0.126 -    0.157: 5
  Chirality restraints: 509
  Sorted by residual:
  chirality pdb=" CA  ILE E 332 "
            pdb=" N   ILE E 332 "
            pdb=" C   ILE E 332 "
            pdb=" CB  ILE E 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.18e-01
  chirality pdb=" CA  PRO L  81 "
            pdb=" N   PRO L  81 "
            pdb=" C   PRO L  81 "
            pdb=" CB  PRO L  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.15 2.00e-01 2.50e+01 5.91e-01
  chirality pdb=" CA  ILE E 434 "
            pdb=" N   ILE E 434 "
            pdb=" C   ILE E 434 "
            pdb=" CB  ILE E 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.87e-01
  ... (remaining 506 not shown)

  Planarity restraints: 605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU L  80 "    0.037 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO L  81 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO L  81 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO L  81 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H  13 "    0.027 5.00e-02 4.00e+02   4.14e-02 2.74e+00
        pdb=" N   PRO H  14 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA H  99 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO H 100 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO H 100 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 100 "    0.023 5.00e-02 4.00e+02
  ... (remaining 602 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 966
        2.81 -     3.33: 2748
        3.33 -     3.85: 4865
        3.85 -     4.38: 5494
        4.38 -     4.90: 10028
  Nonbonded interactions: 24101
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  12 "
            pdb=" O   VAL L 107 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   SER H  86 "
            pdb=" NH1 ARG H  88 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NH1 ARG E 457 "
            pdb=" O   SER E 459 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" NH2 ARG L  55 "
            pdb=" O   ILE L  59 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" NH2 ARG E 493 "
            pdb=" O   GLY H  55 "
     model   vdw
     2.376 3.120
  ... (remaining 24096 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:             4.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.330
  Find NCS groups from input model:        0.010
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
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   0.047   3452  Z= 0.136
  Angle     :  0.707   8.254   4700  Z= 0.374
  Chirality :  0.046   0.157    509
  Planarity :  0.005   0.056    605
  Dihedral  : 13.749  87.928   1227
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.64 (0.40), residues: 425
  helix: -3.48 (0.82), residues: 27
  sheet:  0.31 (0.45), residues: 141
  loop : -1.72 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 498 
 TYR   0.014   0.001   TYR E 453 
 PHE   0.011   0.002   PHE E 515 
 TRP   0.010   0.002   TRP H  48 
 HIS   0.001   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3445)
  covalent geometry    : angle       0.70002 ( 4686)
  SS BOND              : bond        0.00870 (    7)
  SS BOND              : angle       2.00235 (   14)
  hydrogen bonds       : bond        0.19718 (   89)
  hydrogen bonds       : angle       7.72303 (  243)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.126 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0934
  time to fit residues: 7.5459
Evaluate side-chains
  53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN
H   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.167906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.137623 restraints weight = 4394.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.140332 restraints weight = 3282.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.141101 restraints weight = 2245.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.141283 restraints weight = 1983.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.141901 restraints weight = 1746.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3452  Z= 0.200
  Angle     :  0.741   8.335   4700  Z= 0.386
  Chirality :  0.048   0.166    509
  Planarity :  0.006   0.066    605
  Dihedral  :  5.473  28.054    475
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.63 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.40), residues: 425
  helix: -3.25 (0.74), residues: 34
  sheet:  0.44 (0.45), residues: 137
  loop : -1.72 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  88 
 TYR   0.026   0.002   TYR E 453 
 PHE   0.020   0.002   PHE E 490 
 TRP   0.012   0.002   TRP H  48 
 HIS   0.003   0.002   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 3445)
  covalent geometry    : angle       0.73800 ( 4686)
  SS BOND              : bond        0.00855 (    7)
  SS BOND              : angle       1.48580 (   14)
  hydrogen bonds       : bond        0.04103 (   89)
  hydrogen bonds       : angle       5.91410 (  243)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0978
  time to fit residues: 6.7281
Evaluate side-chains
  54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   21 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 30 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 32 optimal weight:    0.3980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.166513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.136092 restraints weight = 4401.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.138352 restraints weight = 3085.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.139131 restraints weight = 2086.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.141710 restraints weight = 1895.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.141736 restraints weight = 1574.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3452  Z= 0.162
  Angle     :  0.691   8.085   4700  Z= 0.359
  Chirality :  0.046   0.168    509
  Planarity :  0.005   0.068    605
  Dihedral  :  5.257  27.549    475
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.44 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.40), residues: 425
  helix: -3.24 (0.71), residues: 34
  sheet:  0.54 (0.45), residues: 137
  loop : -1.75 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 498 
 TYR   0.019   0.002   TYR E 453 
 PHE   0.013   0.002   PHE E 490 
 TRP   0.013   0.002   TRP H  48 
 HIS   0.003   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3445)
  covalent geometry    : angle       0.68735 ( 4686)
  SS BOND              : bond        0.00778 (    7)
  SS BOND              : angle       1.40819 (   14)
  hydrogen bonds       : bond        0.03656 (   89)
  hydrogen bonds       : angle       5.59824 (  243)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 7
  residues processed: 60
  average time/residue: 0.0860
  time to fit residues: 6.0246
Evaluate side-chains
  58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  506 GLN
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   34 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0170
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN
L  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.166043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.135769 restraints weight = 4330.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.137747 restraints weight = 2798.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.138628 restraints weight = 2163.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.138935 restraints weight = 1797.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.139258 restraints weight = 1758.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3452  Z= 0.159
  Angle     :  0.683   8.319   4700  Z= 0.354
  Chirality :  0.046   0.160    509
  Planarity :  0.005   0.069    605
  Dihedral  :  5.151  26.961    475
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 14.71 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.39), residues: 425
  helix: -3.45 (0.70), residues: 33
  sheet:  0.63 (0.44), residues: 137
  loop : -1.72 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  42 
 TYR   0.018   0.002   TYR E 453 
 PHE   0.012   0.002   PHE E 490 
 TRP   0.012   0.002   TRP H  48 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3445)
  covalent geometry    : angle       0.67969 ( 4686)
  SS BOND              : bond        0.00790 (    7)
  SS BOND              : angle       1.45470 (   14)
  hydrogen bonds       : bond        0.03520 (   89)
  hydrogen bonds       : angle       5.41587 (  243)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: L   18 ARG cc_start: 0.7194 (ttp-110) cc_final: 0.6945 (tmm-80)
  outliers start: 19
  outliers final: 9
  residues processed: 69
  average time/residue: 0.0795
  time to fit residues: 6.3807
Evaluate side-chains
  60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  506 GLN
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  112 ASP
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   86 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN
L  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.164183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.134569 restraints weight = 4412.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.137531 restraints weight = 3019.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.138154 restraints weight = 2139.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.138353 restraints weight = 1847.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.138645 restraints weight = 1652.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3452  Z= 0.179
  Angle     :  0.692   8.148   4700  Z= 0.362
  Chirality :  0.046   0.158    509
  Planarity :  0.005   0.069    605
  Dihedral  :  5.275  26.345    475
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 15.80 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.39), residues: 425
  helix: -3.59 (0.68), residues: 33
  sheet:  0.66 (0.45), residues: 137
  loop : -1.74 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 493 
 TYR   0.019   0.002   TYR E 453 
 PHE   0.012   0.002   PHE E 490 
 TRP   0.011   0.002   TRP H  48 
 HIS   0.003   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 3445)
  covalent geometry    : angle       0.68920 ( 4686)
  SS BOND              : bond        0.00837 (    7)
  SS BOND              : angle       1.30693 (   14)
  hydrogen bonds       : bond        0.03776 (   89)
  hydrogen bonds       : angle       5.48201 (  243)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
REVERT: H  109 ASP cc_start: 0.7253 (p0) cc_final: 0.7051 (p0)
REVERT: L   18 ARG cc_start: 0.7327 (ttp-110) cc_final: 0.7034 (tmm-80)
  outliers start: 16
  outliers final: 12
  residues processed: 68
  average time/residue: 0.0645
  time to fit residues: 5.2556
Evaluate side-chains
  63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  354 ASN
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  418 ILE
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue   86 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    0.0070
   chunk 32 optimal weight:    0.1980
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 8 optimal weight:    0.2980
   overall best weight:    0.3198

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

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN
L  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.167491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.137498 restraints weight = 4330.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.139665 restraints weight = 2762.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.139521 restraints weight = 2534.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.140016 restraints weight = 1998.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.140725 restraints weight = 1838.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3452  Z= 0.115
  Angle     :  0.620   7.385   4700  Z= 0.323
  Chirality :  0.044   0.146    509
  Planarity :  0.005   0.067    605
  Dihedral  :  4.946  26.308    475
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.53 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.40), residues: 425
  helix: -3.51 (0.68), residues: 33
  sheet:  0.72 (0.45), residues: 137
  loop : -1.61 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  42 
 TYR   0.012   0.001   TYR H  81 
 PHE   0.011   0.001   PHE E 374 
 TRP   0.011   0.001   TRP E 436 
 HIS   0.001   0.000   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3445)
  covalent geometry    : angle       0.61870 ( 4686)
  SS BOND              : bond        0.00712 (    7)
  SS BOND              : angle       1.00982 (   14)
  hydrogen bonds       : bond        0.02837 (   89)
  hydrogen bonds       : angle       5.21320 (  243)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: L   18 ARG cc_start: 0.7295 (ttp-110) cc_final: 0.6955 (tmm-80)
REVERT: L   82 GLU cc_start: 0.5490 (pp20) cc_final: 0.5281 (pp20)
  outliers start: 13
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0632
  time to fit residues: 4.8151
Evaluate side-chains
  58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   86 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0770
   chunk 29 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0570
   chunk 14 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.4656

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

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.166214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136105 restraints weight = 4437.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.139182 restraints weight = 3156.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.139855 restraints weight = 2143.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.140092 restraints weight = 1919.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.140374 restraints weight = 1692.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3452  Z= 0.134
  Angle     :  0.640   7.483   4700  Z= 0.334
  Chirality :  0.044   0.141    509
  Planarity :  0.005   0.070    605
  Dihedral  :  4.913  25.869    475
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.44 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.40), residues: 425
  helix: -3.22 (0.73), residues: 33
  sheet:  0.74 (0.45), residues: 137
  loop : -1.61 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  42 
 TYR   0.015   0.001   TYR H  81 
 PHE   0.015   0.001   PHE E 374 
 TRP   0.025   0.002   TRP L  36 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3445)
  covalent geometry    : angle       0.63806 ( 4686)
  SS BOND              : bond        0.00777 (    7)
  SS BOND              : angle       1.13949 (   14)
  hydrogen bonds       : bond        0.03199 (   89)
  hydrogen bonds       : angle       5.27206 (  243)

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

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: L   18 ARG cc_start: 0.7343 (ttp-110) cc_final: 0.7000 (tmm-80)
  outliers start: 15
  outliers final: 14
  residues processed: 65
  average time/residue: 0.0781
  time to fit residues: 6.0323
Evaluate side-chains
  68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  354 ASN
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  102 CYS
Chi-restraints excluded: chain H residue  112 ASP
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   86 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4159 > 50:
  distance: 52 - 70:  31.829
  distance: 56 - 78:  31.786
  distance: 59 - 65:  34.494
  distance: 65 - 66:   6.826
  distance: 66 - 67:  42.522
  distance: 66 - 69:  37.075
  distance: 67 - 68:  43.287
  distance: 67 - 70:   5.817
  distance: 70 - 71:  20.253
  distance: 71 - 72:  23.951
  distance: 71 - 74:  14.044
  distance: 72 - 73:  60.450
  distance: 72 - 78:  40.328
  distance: 75 - 77:   8.129
  distance: 78 - 79:  56.957
  distance: 79 - 80:  41.234
  distance: 79 - 82:  46.959
  distance: 80 - 81:  58.354
  distance: 80 - 90:   5.690
  distance: 82 - 83:  34.185
  distance: 83 - 84:  27.721
  distance: 83 - 85:  31.593
  distance: 84 - 86:  14.217
  distance: 86 - 88:   3.078
  distance: 87 - 88:  40.573
  distance: 88 - 89:  11.792
  distance: 90 - 91:   7.649
  distance: 91 - 92:   8.217
  distance: 91 - 94:  22.668
  distance: 92 - 93:  56.488
  distance: 92 - 98:  44.107
  distance: 94 - 95:  18.888
  distance: 95 - 96:  44.053
  distance: 95 - 97:  29.694
  distance: 98 - 99:  37.695
  distance: 99 - 100:  41.546
  distance: 99 - 102:  30.356
  distance: 100 - 101:  47.097
  distance: 100 - 110:  29.609
  distance: 102 - 103:  14.363
  distance: 103 - 104:  14.174
  distance: 103 - 105:  40.285
  distance: 104 - 106:  12.746
  distance: 105 - 107:  43.243
  distance: 106 - 108:  39.394
  distance: 107 - 108:  39.030
  distance: 108 - 109:  40.034
  distance: 110 - 111:  11.410
  distance: 111 - 112:  40.570
  distance: 111 - 114:  41.288
  distance: 112 - 113:  63.844
  distance: 115 - 116:  40.904
  distance: 116 - 117:  53.694
  distance: 117 - 118:  40.266
  distance: 120 - 121:  45.604
  distance: 120 - 123:  55.621
  distance: 121 - 122:  21.280
  distance: 121 - 127:  56.850
  distance: 123 - 124:  36.057
  distance: 124 - 125:  49.936
  distance: 124 - 126:  40.518
  distance: 127 - 128:  53.256
  distance: 127 - 133:  27.928
  distance: 128 - 129:  40.575
  distance: 128 - 131:  41.554
  distance: 129 - 134:  49.676
  distance: 131 - 132:  44.991
  distance: 132 - 133:  14.703
  distance: 134 - 135:  28.420
  distance: 135 - 138:  32.664
  distance: 136 - 137:  46.086
  distance: 136 - 142:  38.589
  distance: 138 - 139:  44.818
  distance: 139 - 140:  31.690
  distance: 139 - 141:  27.588
  distance: 142 - 143:  49.119
  distance: 143 - 144:  43.180
  distance: 143 - 146:  57.757
  distance: 144 - 145:   9.358
  distance: 144 - 150:  28.941
  distance: 146 - 147:  39.910
  distance: 147 - 148:  39.672
  distance: 147 - 149:   8.492