Starting phenix.real_space_refine
on Sat May 10 15:23:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b7q_15899/05_2025/8b7q_15899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b7q_15899/05_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_15899/05_2025/8b7q_15899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b7q_15899/05_2025/8b7q_15899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b7q_15899/05_2025/8b7q_15899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b7q_15899/05_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-5687/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: 3.94, per 1000 atoms: 1.12
  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: 0.86
  Conformation dependent library (CDL) restraints added in 434.5 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: 0.45
  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: 0.99

  Time building geometry restraints manager: 1.01 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:             9.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     14.510
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.220
-------------------------------------------------------------------------------
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   3595  Z= 0.121
  Angle     :  0.601   7.021   4900  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00028 (    1)
  link_NAG-ASN         : angle       1.67786 (    3)
  hydrogen bonds       : bond        0.18058 (  159)
  hydrogen bonds       : angle       7.45858 (  474)
  SS BOND              : bond        0.00220 (    6)
  SS BOND              : angle       0.89249 (   12)
  covalent geometry    : bond        0.00265 ( 3588)
  covalent geometry    : angle       0.59895 ( 4885)

*********************** 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  : 0.425 
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: 0.1647
  time to fit residues: 30.4411
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  : 0.418 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   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 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 = 0.3595 r_free = 0.3595 target = 0.112267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.091981 restraints weight = 8036.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.094698 restraints weight = 4718.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.096656 restraints weight = 3260.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3595  Z= 0.164
  Angle     :  0.671  11.033   4900  Z= 0.341
  Chirality :  0.046   0.261    572
  Planarity :  0.004   0.043    615
  Dihedral  :  4.389  17.576    496
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  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:  1.08 (0.40), residues: 433
  helix:  2.28 (0.50), residues: 103
  sheet:  0.53 (0.40), residues: 127
  loop :  0.11 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 620 
 HIS   0.005   0.001   HIS F 418 
 PHE   0.013   0.002   PHE F 348 
 TYR   0.020   0.002   TYR A  82 
 ARG   0.004   0.000   ARG F 419 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00127 (    1)
  link_NAG-ASN         : angle       2.00761 (    3)
  hydrogen bonds       : bond        0.04163 (  159)
  hydrogen bonds       : angle       5.19963 (  474)
  SS BOND              : bond        0.00494 (    6)
  SS BOND              : angle       3.74568 (   12)
  covalent geometry    : bond        0.00375 ( 3588)
  covalent geometry    : angle       0.64368 ( 4885)

*********************** 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
  115 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8143 (ttpt)
REVERT: A   93 ASN cc_start: 0.7728 (m-40) cc_final: 0.7498 (m-40)
REVERT: B  429 ASN cc_start: 0.8861 (t0) cc_final: 0.8562 (t0)
REVERT: B  572 TYR cc_start: 0.8140 (p90) cc_final: 0.7741 (p90)
REVERT: B  609 VAL cc_start: 0.9504 (t) cc_final: 0.9297 (m)
REVERT: B  612 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8329 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8680 (pt) cc_final: 0.8475 (mm)
REVERT: F  393 ASN cc_start: 0.7555 (t0) cc_final: 0.7053 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1427
  time to fit residues: 19.8550
Evaluate side-chains
  92 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 26 optimal weight:    0.1980
   chunk 22 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   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
** 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.112454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.091841 restraints weight = 8027.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.094388 restraints weight = 4924.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.096162 restraints weight = 3504.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3595  Z= 0.146
  Angle     :  0.633  13.789   4900  Z= 0.324
  Chirality :  0.046   0.230    572
  Planarity :  0.004   0.036    615
  Dihedral  :  4.363  26.095    496
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.21 %
    Favored  : 97.55 %
  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:  1.44 (0.41), residues: 433
  helix:  2.67 (0.50), residues: 102
  sheet:  0.63 (0.41), residues: 129
  loop :  0.39 (0.47), residues: 202

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   0.011   0.001   PHE F 348 
 TYR   0.017   0.001   TYR F 352 
 ARG   0.002   0.000   ARG F 419 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00110 (    1)
  link_NAG-ASN         : angle       2.02336 (    3)
  hydrogen bonds       : bond        0.03900 (  159)
  hydrogen bonds       : angle       4.79317 (  474)
  SS BOND              : bond        0.00902 (    6)
  SS BOND              : angle       3.29455 (   12)
  covalent geometry    : bond        0.00337 ( 3588)
  covalent geometry    : angle       0.61035 ( 4885)

*********************** 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
  106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8316 (ttpt)
REVERT: B  429 ASN cc_start: 0.8918 (t0) cc_final: 0.8601 (t0)
REVERT: B  609 VAL cc_start: 0.9440 (t) cc_final: 0.9206 (m)
REVERT: B  612 ARG cc_start: 0.8874 (ttt180) cc_final: 0.8461 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8640 (pt) cc_final: 0.8327 (mm)
REVERT: F  393 ASN cc_start: 0.7703 (t0) cc_final: 0.6976 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1592
  time to fit residues: 20.6270
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  : 0.449 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 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 = 0.3592 r_free = 0.3592 target = 0.112101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.091670 restraints weight = 8061.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.094265 restraints weight = 4943.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.096107 restraints weight = 3505.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.4385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3595  Z= 0.133
  Angle     :  0.614  11.985   4900  Z= 0.310
  Chirality :  0.045   0.195    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.396  24.948    496
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.21 %
    Favored  : 97.55 %
  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:  1.50 (0.41), residues: 433
  helix:  2.89 (0.50), residues: 102
  sheet:  0.82 (0.42), residues: 128
  loop :  0.19 (0.47), residues: 203

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   0.009   0.001   PHE F 348 
 TYR   0.018   0.001   TYR B 572 
 ARG   0.003   0.000   ARG F 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00071 (    1)
  link_NAG-ASN         : angle       2.06252 (    3)
  hydrogen bonds       : bond        0.03756 (  159)
  hydrogen bonds       : angle       4.60494 (  474)
  SS BOND              : bond        0.00551 (    6)
  SS BOND              : angle       3.18702 (   12)
  covalent geometry    : bond        0.00312 ( 3588)
  covalent geometry    : angle       0.59219 ( 4885)

*********************** 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
  101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8207 (ttpt)
REVERT: B  429 ASN cc_start: 0.8934 (t0) cc_final: 0.8633 (t0)
REVERT: B  542 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8264 (mmtm)
REVERT: B  612 ARG cc_start: 0.8912 (ttt180) cc_final: 0.8576 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8640 (pt) cc_final: 0.8288 (mm)
REVERT: F  393 ASN cc_start: 0.7598 (t0) cc_final: 0.6769 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1490
  time to fit residues: 18.4126
Evaluate side-chains
  83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0770
   chunk 24 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0970
   chunk 4 optimal weight:    0.4980
   chunk 18 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.5336

-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.111723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.090770 restraints weight = 8250.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.093504 restraints weight = 4950.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.095391 restraints weight = 3452.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3595  Z= 0.123
  Angle     :  0.606  11.588   4900  Z= 0.308
  Chirality :  0.044   0.184    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.429  32.361    496
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  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:  1.50 (0.41), residues: 433
  helix:  3.00 (0.51), residues: 102
  sheet:  0.85 (0.42), residues: 127
  loop :  0.11 (0.47), residues: 204

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 348 
 TYR   0.009   0.001   TYR F 424 
 ARG   0.004   0.000   ARG F 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00057 (    1)
  link_NAG-ASN         : angle       2.03906 (    3)
  hydrogen bonds       : bond        0.03613 (  159)
  hydrogen bonds       : angle       4.43068 (  474)
  SS BOND              : bond        0.00524 (    6)
  SS BOND              : angle       3.54311 (   12)
  covalent geometry    : bond        0.00283 ( 3588)
  covalent geometry    : angle       0.57926 ( 4885)

*********************** 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
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.581 
Fit side-chains
REVERT: A   69 ILE cc_start: 0.7172 (tp) cc_final: 0.6847 (tp)
REVERT: A   74 LYS cc_start: 0.8547 (ttpt) cc_final: 0.8289 (ttpt)
REVERT: B  429 ASN cc_start: 0.8917 (t0) cc_final: 0.8624 (t0)
REVERT: B  453 GLN cc_start: 0.8709 (pt0) cc_final: 0.8305 (pm20)
REVERT: B  542 LYS cc_start: 0.8546 (mmmm) cc_final: 0.8234 (mmtm)
REVERT: B  572 TYR cc_start: 0.7986 (p90) cc_final: 0.7629 (p90)
REVERT: B  612 ARG cc_start: 0.8866 (ttt180) cc_final: 0.8515 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8637 (pt) cc_final: 0.8330 (mm)
REVERT: F  393 ASN cc_start: 0.7577 (t0) cc_final: 0.6454 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1512
  time to fit residues: 18.3969
Evaluate side-chains
  84 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 ** 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 = 0.3534 r_free = 0.3534 target = 0.109246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.088529 restraints weight = 8426.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.091103 restraints weight = 5247.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.092912 restraints weight = 3726.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3595  Z= 0.166
  Angle     :  0.640  10.478   4900  Z= 0.325
  Chirality :  0.046   0.188    572
  Planarity :  0.004   0.027    615
  Dihedral  :  4.647  33.435    496
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    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:  1.31 (0.41), residues: 433
  helix:  3.11 (0.50), residues: 96
  sheet:  0.74 (0.42), residues: 128
  loop : -0.09 (0.45), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 465 
 PHE   0.011   0.001   PHE F 348 
 TYR   0.013   0.001   TYR F 424 
 ARG   0.005   0.000   ARG F 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00208 (    1)
  link_NAG-ASN         : angle       2.45846 (    3)
  hydrogen bonds       : bond        0.03862 (  159)
  hydrogen bonds       : angle       4.69863 (  474)
  SS BOND              : bond        0.00497 (    6)
  SS BOND              : angle       3.66687 (   12)
  covalent geometry    : bond        0.00385 ( 3588)
  covalent geometry    : angle       0.61215 ( 4885)

*********************** 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  : 0.390 
Fit side-chains
REVERT: A   69 ILE cc_start: 0.7169 (tp) cc_final: 0.6909 (tp)
REVERT: A   74 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8256 (ttpt)
REVERT: B  429 ASN cc_start: 0.8877 (t0) cc_final: 0.8605 (t0)
REVERT: B  453 GLN cc_start: 0.8757 (pt0) cc_final: 0.8194 (pm20)
REVERT: B  542 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8306 (mmtm)
REVERT: B  572 TYR cc_start: 0.8057 (p90) cc_final: 0.7662 (p90)
REVERT: B  612 ARG cc_start: 0.8902 (ttt180) cc_final: 0.8537 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7530 (t0) cc_final: 0.6656 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1498
  time to fit residues: 18.0269
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  : 0.390 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0970
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.111532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.090981 restraints weight = 8049.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.093554 restraints weight = 4929.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.095318 restraints weight = 3486.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.5032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3595  Z= 0.126
  Angle     :  0.596   9.426   4900  Z= 0.302
  Chirality :  0.044   0.161    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.420  30.703    496
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  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:  1.33 (0.41), residues: 433
  helix:  2.54 (0.52), residues: 108
  sheet:  0.94 (0.43), residues: 127
  loop : -0.05 (0.46), residues: 198

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   0.008   0.001   PHE F 334 
 TYR   0.009   0.001   TYR F 424 
 ARG   0.007   0.000   ARG F 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00070 (    1)
  link_NAG-ASN         : angle       2.19495 (    3)
  hydrogen bonds       : bond        0.03603 (  159)
  hydrogen bonds       : angle       4.44779 (  474)
  SS BOND              : bond        0.00405 (    6)
  SS BOND              : angle       3.16892 (   12)
  covalent geometry    : bond        0.00292 ( 3588)
  covalent geometry    : angle       0.57339 ( 4885)

*********************** 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  : 0.411 
Fit side-chains
REVERT: A   69 ILE cc_start: 0.7103 (tp) cc_final: 0.6604 (tp)
REVERT: A   74 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8247 (ttpt)
REVERT: B  429 ASN cc_start: 0.8833 (t0) cc_final: 0.8555 (t0)
REVERT: B  453 GLN cc_start: 0.8661 (pt0) cc_final: 0.8128 (pm20)
REVERT: B  542 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8331 (mmtm)
REVERT: B  572 TYR cc_start: 0.8048 (p90) cc_final: 0.7643 (p90)
REVERT: B  612 ARG cc_start: 0.8879 (ttt180) cc_final: 0.8415 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7558 (t0) cc_final: 0.6685 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1524
  time to fit residues: 18.1897
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  : 0.402 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 37 optimal weight:    0.0570
   chunk 26 optimal weight:    0.0050
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5512

-------------------------------------------------------------------------------
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
B 499 GLN
** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.111528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.091536 restraints weight = 8145.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.094022 restraints weight = 4985.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.095754 restraints weight = 3531.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.5128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3595  Z= 0.123
  Angle     :  0.598   9.281   4900  Z= 0.304
  Chirality :  0.045   0.175    572
  Planarity :  0.003   0.028    615
  Dihedral  :  4.447  34.515    496
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  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:  1.40 (0.41), residues: 433
  helix:  2.54 (0.51), residues: 108
  sheet:  1.09 (0.44), residues: 125
  loop : -0.04 (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 465 
 PHE   0.008   0.001   PHE F 334 
 TYR   0.010   0.001   TYR F 424 
 ARG   0.001   0.000   ARG B 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00070 (    1)
  link_NAG-ASN         : angle       2.08790 (    3)
  hydrogen bonds       : bond        0.03658 (  159)
  hydrogen bonds       : angle       4.55599 (  474)
  SS BOND              : bond        0.00365 (    6)
  SS BOND              : angle       3.55589 (   12)
  covalent geometry    : bond        0.00285 ( 3588)
  covalent geometry    : angle       0.57006 ( 4885)

*********************** 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
  94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A   69 ILE cc_start: 0.7092 (tp) cc_final: 0.6644 (tp)
REVERT: A   74 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8227 (ttpt)
REVERT: B  429 ASN cc_start: 0.8824 (t0) cc_final: 0.8580 (t0)
REVERT: B  542 LYS cc_start: 0.8575 (mmmm) cc_final: 0.8339 (mmtm)
REVERT: B  612 ARG cc_start: 0.8903 (ttt180) cc_final: 0.8415 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7584 (t0) cc_final: 0.6696 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1505
  time to fit residues: 17.5442
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  : 0.415 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    1.0982

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.108931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.089010 restraints weight = 8166.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.091424 restraints weight = 5098.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.093127 restraints weight = 3645.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.5297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3595  Z= 0.195
  Angle     :  0.677  10.359   4900  Z= 0.344
  Chirality :  0.047   0.190    572
  Planarity :  0.004   0.032    615
  Dihedral  :  4.866  38.140    496
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  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:  1.24 (0.41), residues: 433
  helix:  2.59 (0.51), residues: 102
  sheet:  0.88 (0.44), residues: 128
  loop : -0.09 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 447 
 HIS   0.006   0.001   HIS B 465 
 PHE   0.015   0.002   PHE F 334 
 TYR   0.014   0.002   TYR F 424 
 ARG   0.002   0.000   ARG F 385 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00323 (    1)
  link_NAG-ASN         : angle       2.76493 (    3)
  hydrogen bonds       : bond        0.04018 (  159)
  hydrogen bonds       : angle       4.85067 (  474)
  SS BOND              : bond        0.00564 (    6)
  SS BOND              : angle       3.89948 (   12)
  covalent geometry    : bond        0.00448 ( 3588)
  covalent geometry    : angle       0.64590 ( 4885)

*********************** 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
  99 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ILE cc_start: 0.7066 (tp) cc_final: 0.5778 (tp)
REVERT: A   74 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8239 (ttpt)
REVERT: B  429 ASN cc_start: 0.8815 (t0) cc_final: 0.8588 (t0)
REVERT: B  612 ARG cc_start: 0.8957 (ttt180) cc_final: 0.8640 (ttt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1515
  time to fit residues: 18.5125
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  : 0.440 
-------------------------------------------------------------------------------
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-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 64.1849 > 50:
  distance: 21 - 42:   4.319
  distance: 25 - 50:   8.352
  distance: 30 - 55:  26.849
  distance: 36 - 42:   4.191
  distance: 42 - 43:   8.767
  distance: 43 - 44:  18.143
  distance: 43 - 46:  10.826
  distance: 44 - 45:  20.103
  distance: 44 - 50:  11.645
  distance: 46 - 47:   9.803
  distance: 47 - 48:  11.006
  distance: 47 - 49:  21.069
  distance: 50 - 51:  13.917
  distance: 51 - 52:  34.319
  distance: 51 - 54:  12.695
  distance: 52 - 53:  24.322
  distance: 52 - 55:  47.476
  distance: 55 - 56:  39.185
  distance: 56 - 57:  25.940
  distance: 56 - 59:  54.366
  distance: 57 - 58:  16.171
  distance: 57 - 66:  28.979
  distance: 59 - 60:  62.824
  distance: 60 - 61:  46.894
  distance: 60 - 62:  54.398
  distance: 61 - 63:  39.701
  distance: 63 - 65:  23.560
  distance: 64 - 65:  23.791
  distance: 66 - 67:  20.391
  distance: 67 - 68:  33.328
  distance: 67 - 70:   9.487
  distance: 68 - 69:  43.440
  distance: 68 - 72:  24.099
  distance: 70 - 71:  22.308
  distance: 72 - 73:  10.124
  distance: 73 - 74:  12.096
  distance: 73 - 76:  11.091
  distance: 74 - 75:  11.089
  distance: 74 - 81:   8.064
  distance: 76 - 77:  13.185
  distance: 77 - 78:  15.320
  distance: 78 - 79:  12.836
  distance: 79 - 80:   8.477
  distance: 81 - 82:  13.919
  distance: 82 - 83:  13.881
  distance: 82 - 85:  23.691
  distance: 83 - 84:  19.149
  distance: 83 - 87:  15.007
  distance: 85 - 86:   6.395
  distance: 87 - 88:  37.803
  distance: 88 - 89:  26.584
  distance: 88 - 91:  21.768
  distance: 89 - 90:  10.860
  distance: 89 - 93:   6.535
  distance: 91 - 92:  26.740
  distance: 92 - 121:  24.336
  distance: 93 - 94:  10.015
  distance: 94 - 95:  14.237
  distance: 94 - 97:  26.158
  distance: 97 - 98:   8.461
  distance: 99 - 100:  58.241
  distance: 100 - 101:  41.982
  distance: 100 - 103:  64.185
  distance: 101 - 102:  14.178
  distance: 101 - 107:  28.885
  distance: 103 - 104:  52.135
  distance: 104 - 105:  10.574
  distance: 104 - 106:  35.876
  distance: 107 - 108:  24.232
  distance: 107 - 113:   8.823
  distance: 108 - 109:  15.124
  distance: 108 - 111:   7.589
  distance: 109 - 110:  12.899
  distance: 111 - 112:  13.345
  distance: 112 - 113:  26.159