Starting phenix.real_space_refine
on Fri Aug 22 23:06:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jk4_61543/08_2025/9jk4_61543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jk4_61543/08_2025/9jk4_61543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jk4_61543/08_2025/9jk4_61543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jk4_61543/08_2025/9jk4_61543.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jk4_61543/08_2025/9jk4_61543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jk4_61543/08_2025/9jk4_61543.map"
  }
  resolution = 2.82
  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=  -0.002 sd=   0.085
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      63      5.16       5
     C    5382      2.51       5
     N    1421      2.21       5
     O    1491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  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: 8358
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1048, 8250
          Classifications: {'peptide': 1048}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 54, 'TRANS': 993}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.48, per 1000 atoms: 0.18
  Number of scatterers: 8358
  At special positions: 0
  Unit cell: (81.2446, 86.7341, 162.489, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     P       1     15.00
     O    1491      8.00
     N    1421      7.00
     C    5382      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A1202 "
      " NAG C   1 " - " ASN A1205 "
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 208.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1990

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 6 sheets defined
      57.3% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 44
    Processing helix  chain 'A' and resid 46 through 54
    Processing helix  chain 'A' and resid 66 through 82
    Processing helix  chain 'A' and resid 93 through 122
      removed outlier: 3.515A  pdb=" N   VAL A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 141
    Processing helix  chain 'A' and resid 148 through 152
      removed outlier: 3.752A  pdb=" N   TYR A 152 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 249 through 260
      removed outlier: 4.288A  pdb=" N   ASN A 253 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 302
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 309 through 323
    Processing helix  chain 'A' and resid 324 through 326
      No H-bonds generated for 'chain 'A' and resid 324 through 326'
    Processing helix  chain 'A' and resid 329 through 350
    Processing helix  chain 'A' and resid 375 through 392
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 578 through 594
      Proline residue:  A 584  - end of helix
    Processing helix  chain 'A' and resid 595 through 616
      removed outlier: 3.528A  pdb=" N   GLU A 600 " --> pdb=" O   ALA A 596 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ARG A 601 " --> pdb=" O   SER A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 638
      removed outlier: 3.511A  pdb=" N   ALA A 634 " --> pdb=" O   LEU A 630 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 645
      removed outlier: 3.570A  pdb=" N   LYS A 644 " --> pdb=" O   PRO A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 726 through 744
      removed outlier: 3.550A  pdb=" N   LEU A 742 " --> pdb=" O   GLN A 738 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   SER A 743 " --> pdb=" O   ARG A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 763
    Processing helix  chain 'A' and resid 814 through 819
    Processing helix  chain 'A' and resid 834 through 847
      removed outlier: 3.545A  pdb=" N   ASN A 846 " --> pdb=" O   ASP A 842 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA A 847 " --> pdb=" O   GLY A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 869
      removed outlier: 4.051A  pdb=" N   VAL A 864 " --> pdb=" O   LEU A 860 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE A 865 " --> pdb=" O   LYS A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 965
      removed outlier: 3.574A  pdb=" N   VAL A 958 " --> pdb=" O   GLY A 954 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   ARG A 959 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      Proline residue:  A 960  - end of helix
    Processing helix  chain 'A' and resid 979 through 993
      removed outlier: 3.516A  pdb=" N   TYR A 993 " --> pdb=" O   ILE A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1015
      removed outlier: 4.519A  pdb=" N   LEU A1011 " --> pdb=" O   ARG A1007 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN A1014 " --> pdb=" O   CYS A1010 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER A1015 " --> pdb=" O   LEU A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1050 through 1060
      removed outlier: 3.528A  pdb=" N   LEU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1073
      No H-bonds generated for 'chain 'A' and resid 1071 through 1073'
    Processing helix  chain 'A' and resid 1074 through 1114
      removed outlier: 3.533A  pdb=" N   LEU A1103 " --> pdb=" O   CYS A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1130
    Processing helix  chain 'A' and resid 1130 through 1138
    Processing helix  chain 'A' and resid 1139 through 1141
      No H-bonds generated for 'chain 'A' and resid 1139 through 1141'
    Processing helix  chain 'A' and resid 1147 through 1151
      removed outlier: 3.847A  pdb=" N   MET A1151 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1161 through 1201
      removed outlier: 5.171A  pdb=" N   LEU A1178 " --> pdb=" O   LEU A1174 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   THR A1179 " --> pdb=" O   LYS A1175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1225 through 1252
      removed outlier: 4.080A  pdb=" N   THR A1250 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   HIS A1251 " --> pdb=" O   ILE A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1265
    Processing helix  chain 'A' and resid 1266 through 1291
      Proline residue:  A1274  - end of helix
    Processing helix  chain 'A' and resid 1306 through 1348
      removed outlier: 3.626A  pdb=" N   TRP A1310 " --> pdb=" O   PRO A1306 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A1317 " --> pdb=" O   GLY A1313 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL A1318 " --> pdb=" O   CYS A1314 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 178
      removed outlier: 4.231A  pdb=" N   TRP A 167 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 200 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 879 through 880
      removed outlier: 6.344A  pdb=" N   ILE A 879 " --> pdb=" O   THR A 976 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   PHE A 975 " --> pdb=" O   PHE A 851 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   TYR A 853 " --> pdb=" O   PHE A 975 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL A 412 " --> pdb=" O   CYS A 998 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   LEU A1000 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   CYS A 414 " --> pdb=" O   LEU A1000 " (cutoff:3.500A)
      removed outlier: 8.592A  pdb=" N   SER A1002 " --> pdb=" O   CYS A 414 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   THR A 997 " --> pdb=" O   ILE A1017 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   ILE A1019 " --> pdb=" O   THR A 997 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   CYS A 999 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   LEU A1021 " --> pdb=" O   CYS A 999 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   GLY A1001 " --> pdb=" O   LEU A1021 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 552 through 557
      removed outlier: 3.924A  pdb=" N   GLU A 554 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   PHE A 434 " --> pdb=" O   GLU A 554 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU A 556 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   GLN A 830 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A 431 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   GLY A 825 " --> pdb=" O   PHE A 749 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   PHE A 749 " --> pdb=" O   GLY A 825 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   GLN A 821 " --> pdb=" O   CYS A 713 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP A 715 " --> pdb=" O   GLN A 821 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 557
      removed outlier: 3.924A  pdb=" N   GLU A 554 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   PHE A 434 " --> pdb=" O   GLU A 554 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU A 556 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   GLN A 830 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A 431 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   GLY A 825 " --> pdb=" O   PHE A 749 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   PHE A 749 " --> pdb=" O   GLY A 825 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER A 702 " --> pdb=" O   ALA A 750 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LYS A 752 " --> pdb=" O   MET A 700 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   SER A 683 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   LYS A 691 " --> pdb=" O   GLN A 649 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   GLN A 649 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 9.035A  pdb=" N   ILE A 767 " --> pdb=" O   HIS A 652 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ALA A 654 " --> pdb=" O   ILE A 767 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU A 769 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TYR A 656 " --> pdb=" O   LEU A 769 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 559 through 560
    Processing sheet with id=AA6, first strand: chain 'A' and resid 756 through 757

    480 hydrogen bonds defined for protein.
    1389 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.56

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1496
        1.33 -     1.45: 2092
        1.45 -     1.57: 4869
        1.57 -     1.70: 2
        1.70 -     1.82: 85
  Bond restraints: 8544
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 5.08e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.16e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.09e+00
  bond pdb=" C3  NAG B   1 "
       pdb=" O3  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.424 -0.021 2.00e-02 2.50e+03 1.08e+00
  ... (remaining 8539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 11482
        2.36 -     4.73: 107
        4.73 -     7.09: 10
        7.09 -     9.46: 1
        9.46 -    11.82: 1
  Bond angle restraints: 11601
  Sorted by residual:
  angle pdb=" CB  MET A 555 "
        pdb=" CG  MET A 555 "
        pdb=" SD  MET A 555 "
      ideal   model   delta    sigma   weight residual
     112.70  124.52  -11.82 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" N   GLN A1289 "
        pdb=" CA  GLN A1289 "
        pdb=" C   GLN A1289 "
      ideal   model   delta    sigma   weight residual
     113.88  109.33    4.55 1.23e+00 6.61e-01 1.37e+01
  angle pdb=" C   LEU A1288 "
        pdb=" CA  LEU A1288 "
        pdb=" CB  LEU A1288 "
      ideal   model   delta    sigma   weight residual
     110.27  104.71    5.56 1.94e+00 2.66e-01 8.20e+00
  angle pdb=" CB  MET A 826 "
        pdb=" CG  MET A 826 "
        pdb=" SD  MET A 826 "
      ideal   model   delta    sigma   weight residual
     112.70  120.89   -8.19 3.00e+00 1.11e-01 7.46e+00
  angle pdb=" CG  MET A 826 "
        pdb=" SD  MET A 826 "
        pdb=" CE  MET A 826 "
      ideal   model   delta    sigma   weight residual
     100.90  106.48   -5.58 2.20e+00 2.07e-01 6.43e+00
  ... (remaining 11596 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.15: 4582
       21.15 -    42.30: 476
       42.30 -    63.45: 107
       63.45 -    84.60: 12
       84.60 -   105.75: 12
  Dihedral angle restraints: 5189
    sinusoidal: 2142
      harmonic: 3047
  Sorted by residual:
  dihedral pdb=" C2  NAG B   2 "
           pdb=" C3  NAG B   2 "
           pdb=" C4  NAG B   2 "
           pdb=" O4  NAG B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   69.36  105.75     1      3.00e+01 1.11e-03 1.36e+01
  dihedral pdb=" C2  NAG B   2 "
           pdb=" C3  NAG B   2 "
           pdb=" C4  NAG B   2 "
           pdb=" C5  NAG B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -51.56  105.34     1      3.00e+01 1.11e-03 1.35e+01
  dihedral pdb=" O3  NAG B   2 "
           pdb=" C3  NAG B   2 "
           pdb=" C4  NAG B   2 "
           pdb=" O4  NAG B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.55 -169.21  104.66     1      3.00e+01 1.11e-03 1.34e+01
  ... (remaining 5186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 953
       0.034 -    0.069: 312
       0.069 -    0.103: 73
       0.103 -    0.138: 27
       0.138 -    0.172: 3
  Chirality restraints: 1368
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A1202 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.57    0.17 2.00e-01 2.50e+01 7.40e-01
  chirality pdb=" CA  ASN A 876 "
            pdb=" N   ASN A 876 "
            pdb=" C   ASN A 876 "
            pdb=" CB  ASN A 876 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" C4  NAG B   1 "
            pdb=" C3  NAG B   1 "
            pdb=" C5  NAG B   1 "
            pdb=" O4  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.39   -0.14 2.00e-01 2.50e+01 4.91e-01
  ... (remaining 1365 not shown)

  Planarity restraints: 1442
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 313 "    0.014 2.00e-02 2.50e+03   2.88e-02 8.32e+00
        pdb=" C   THR A 313 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   THR A 313 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LEU A 314 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 281 "    0.011 2.00e-02 2.50e+03   2.32e-02 5.37e+00
        pdb=" C   LEU A 281 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   LEU A 281 "    0.015 2.00e-02 2.50e+03
        pdb=" N   HIS A 282 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 157 "    0.029 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO A 158 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 158 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 158 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1439 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1820
        2.78 -     3.31: 7595
        3.31 -     3.84: 13650
        3.84 -     4.37: 15961
        4.37 -     4.90: 28257
  Nonbonded interactions: 67283
  Sorted by model distance:
  nonbonded pdb=" O   SER A1050 "
            pdb=" OG  SER A1050 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   GLN A1289 "
            pdb=" NH2 ARG A1294 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" O   TRP A 875 "
            pdb=" ND2 ASN A 876 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   ASP A 595 "
            pdb=" OG1 THR A 599 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   PHE A1012 "
            pdb=" OG  SER A1018 "
     model   vdw
     2.291 3.040
  ... (remaining 67278 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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 individual isotropic
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:             2.330
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.740
  Find NCS groups from input model:        0.050
  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:8.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
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   0.045   8548  Z= 0.144
  Angle     :  0.567  11.825  11613  Z= 0.277
  Chirality :  0.038   0.172   1368
  Planarity :  0.004   0.045   1440
  Dihedral  : 17.967 105.749   3199
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 21.13 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.87 (0.27), residues: 1030
  helix:  1.38 (0.23), residues: 540
  sheet: -1.09 (0.45), residues: 111
  loop :  0.09 (0.34), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 601 
 TYR   0.013   0.001   TYR A 312 
 PHE   0.009   0.001   PHE A 292 
 TRP   0.025   0.001   TRP A 875 
 HIS   0.003   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8544)
  covalent geometry    : angle       0.55917 (11601)
  hydrogen bonds       : bond        0.22726 (  470)
  hydrogen bonds       : angle       6.85083 ( 1389)
  link_BETA1-4         : bond        0.00268 (    2)
  link_BETA1-4         : angle       2.54058 (    6)
  link_NAG-ASN         : bond        0.00338 (    2)
  link_NAG-ASN         : angle       3.37453 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  754 MET cc_start: 0.0537 (mtp) cc_final: -0.1149 (tpp)
REVERT: A  981 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6951 (mp0)
REVERT: A 1345 GLN cc_start: 0.7574 (mt0) cc_final: 0.6893 (mm-40)
  outliers start: 20
  outliers final: 11
  residues processed: 94
  average time/residue: 0.4472
  time to fit residues: 44.8198
Evaluate side-chains
  86 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  981 GLU
Chi-restraints excluded: chain A residue 1060 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1193 SER
Chi-restraints excluded: chain A residue 1224 ASP
Chi-restraints excluded: chain A residue 1320 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.0060
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 282 HIS
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 GLN
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 830 GLN
A 876 ASN
A 956 HIS
A 957 GLN
A1014 GLN
** A1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1214 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.181429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.104023 restraints weight = 9523.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.23
r_work: 0.3123 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8548  Z= 0.147
  Angle     :  0.602  11.014  11613  Z= 0.296
  Chirality :  0.041   0.191   1368
  Planarity :  0.005   0.043   1440
  Dihedral  :  9.413  87.626   1258
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 17.72 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.44 (0.27), residues: 1030
  helix:  2.05 (0.22), residues: 558
  sheet: -1.12 (0.45), residues: 109
  loop : -0.02 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.013   0.001   TYR A 312 
 PHE   0.029   0.002   PHE A 823 
 TRP   0.011   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8544)
  covalent geometry    : angle       0.59748 (11601)
  hydrogen bonds       : bond        0.06367 (  470)
  hydrogen bonds       : angle       4.63322 ( 1389)
  link_BETA1-4         : bond        0.00397 (    2)
  link_BETA1-4         : angle       2.18229 (    6)
  link_NAG-ASN         : bond        0.00252 (    2)
  link_NAG-ASN         : angle       2.49439 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 83
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  433 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6074 (pp)
REVERT: A  602 LEU cc_start: -0.0741 (OUTLIER) cc_final: -0.1306 (mt)
REVERT: A  754 MET cc_start: 0.0763 (mtp) cc_final: -0.0692 (tpp)
REVERT: A  872 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7512 (mp0)
  outliers start: 44
  outliers final: 16
  residues processed: 115
  average time/residue: 0.4094
  time to fit residues: 50.6133
Evaluate side-chains
  92 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1302 LEU
Chi-restraints excluded: chain A residue 1320 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 277 GLN
A 282 HIS
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 956 HIS
A1214 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.180655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.114619 restraints weight = 9364.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.27
r_work: 0.3069 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8548  Z= 0.153
  Angle     :  0.595   9.045  11613  Z= 0.288
  Chirality :  0.040   0.162   1368
  Planarity :  0.004   0.043   1440
  Dihedral  :  7.702  83.442   1246
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 18.14 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.66 (0.27), residues: 1030
  helix:  2.31 (0.22), residues: 558
  sheet: -1.07 (0.46), residues: 109
  loop : -0.05 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1254 
 TYR   0.013   0.001   TYR A 312 
 PHE   0.022   0.002   PHE A 823 
 TRP   0.010   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8544)
  covalent geometry    : angle       0.59046 (11601)
  hydrogen bonds       : bond        0.05849 (  470)
  hydrogen bonds       : angle       4.41671 ( 1389)
  link_BETA1-4         : bond        0.00267 (    2)
  link_BETA1-4         : angle       2.06012 (    6)
  link_NAG-ASN         : bond        0.00660 (    2)
  link_NAG-ASN         : angle       2.67784 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 79
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A   48 LYS cc_start: 0.7875 (tptt) cc_final: 0.7502 (mmpt)
REVERT: A  122 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7865 (mmm-85)
REVERT: A  433 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6170 (pp)
REVERT: A  602 LEU cc_start: -0.0665 (OUTLIER) cc_final: -0.1256 (mt)
REVERT: A  754 MET cc_start: 0.0791 (mtp) cc_final: -0.0507 (tpp)
REVERT: A  872 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7652 (mp0)
REVERT: A 1070 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7960 (pm20)
REVERT: A 1340 LYS cc_start: 0.8563 (mttm) cc_final: 0.7907 (tmmm)
  outliers start: 43
  outliers final: 19
  residues processed: 109
  average time/residue: 0.4014
  time to fit residues: 47.0758
Evaluate side-chains
  98 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  879 ILE
Chi-restraints excluded: chain A residue 1070 GLU
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1151 MET
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1302 LEU
Chi-restraints excluded: chain A residue 1341 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 47 optimal weight:    0.3980
   chunk 42 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 282 HIS
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 956 HIS
A1214 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.180880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.113952 restraints weight = 9579.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.53
r_work: 0.3073 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8548  Z= 0.141
  Angle     :  0.573   9.487  11613  Z= 0.279
  Chirality :  0.040   0.168   1368
  Planarity :  0.004   0.043   1440
  Dihedral  :  6.987  78.935   1241
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 18.68 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.77 (0.27), residues: 1030
  helix:  2.41 (0.22), residues: 559
  sheet: -1.07 (0.45), residues: 109
  loop : -0.00 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1068 
 TYR   0.013   0.001   TYR A 312 
 PHE   0.020   0.001   PHE A 823 
 TRP   0.010   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8544)
  covalent geometry    : angle       0.56876 (11601)
  hydrogen bonds       : bond        0.05352 (  470)
  hydrogen bonds       : angle       4.27772 ( 1389)
  link_BETA1-4         : bond        0.00311 (    2)
  link_BETA1-4         : angle       2.19451 (    6)
  link_NAG-ASN         : bond        0.00377 (    2)
  link_NAG-ASN         : angle       2.36465 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 76
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LYS cc_start: 0.7950 (tptt) cc_final: 0.7624 (mmpt)
REVERT: A  118 ARG cc_start: 0.7270 (ttm170) cc_final: 0.6684 (ttm-80)
REVERT: A  122 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7832 (mtt180)
REVERT: A  404 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8066 (tp)
REVERT: A  433 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6166 (pp)
REVERT: A  555 MET cc_start: 0.3940 (mmp) cc_final: 0.3510 (mmm)
REVERT: A  602 LEU cc_start: -0.0639 (OUTLIER) cc_final: -0.1221 (mt)
REVERT: A  754 MET cc_start: 0.1050 (mtp) cc_final: -0.0420 (tpp)
REVERT: A  781 MET cc_start: 0.0212 (ppp) cc_final: -0.0194 (ptp)
REVERT: A  872 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7655 (mp0)
REVERT: A  959 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7406 (ttm170)
REVERT: A 1320 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7703 (m)
REVERT: A 1340 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7893 (tmmm)
  outliers start: 42
  outliers final: 17
  residues processed: 104
  average time/residue: 0.3864
  time to fit residues: 43.1548
Evaluate side-chains
  95 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  824 MET
Chi-restraints excluded: chain A residue  842 ASP
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  879 ILE
Chi-restraints excluded: chain A residue  959 ARG
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1302 LEU
Chi-restraints excluded: chain A residue 1320 VAL
Chi-restraints excluded: chain A residue 1340 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0060
   chunk 37 optimal weight:   20.0000
   chunk 100 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 54 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 91 optimal weight:    0.7980
   chunk 101 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 282 HIS
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 956 HIS
A1214 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.181095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.104558 restraints weight = 9494.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.18
r_work: 0.3130 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8548  Z= 0.130
  Angle     :  0.557   9.475  11613  Z= 0.272
  Chirality :  0.039   0.169   1368
  Planarity :  0.004   0.043   1440
  Dihedral  :  6.766  75.400   1240
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 19.10 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.87 (0.27), residues: 1030
  helix:  2.49 (0.22), residues: 560
  sheet: -1.04 (0.44), residues: 114
  loop :  0.04 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1068 
 TYR   0.012   0.001   TYR A 312 
 PHE   0.022   0.001   PHE A 823 
 TRP   0.010   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8544)
  covalent geometry    : angle       0.55201 (11601)
  hydrogen bonds       : bond        0.05104 (  470)
  hydrogen bonds       : angle       4.20353 ( 1389)
  link_BETA1-4         : bond        0.00304 (    2)
  link_BETA1-4         : angle       2.28519 (    6)
  link_NAG-ASN         : bond        0.00301 (    2)
  link_NAG-ASN         : angle       2.28131 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 74
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LYS cc_start: 0.7819 (tptt) cc_final: 0.7556 (mmpt)
REVERT: A  118 ARG cc_start: 0.7210 (ttm170) cc_final: 0.6563 (ttm-80)
REVERT: A  122 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7653 (mtt180)
REVERT: A  404 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7959 (tp)
REVERT: A  433 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6200 (pp)
REVERT: A  555 MET cc_start: 0.3929 (mmp) cc_final: 0.3540 (mmm)
REVERT: A  602 LEU cc_start: -0.0543 (OUTLIER) cc_final: -0.1124 (mt)
REVERT: A  700 MET cc_start: 0.0248 (ptt) cc_final: -0.0392 (ttt)
REVERT: A  754 MET cc_start: 0.1270 (mtp) cc_final: -0.0120 (tpp)
REVERT: A  781 MET cc_start: 0.0200 (ppp) cc_final: -0.0249 (ptp)
REVERT: A  872 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7574 (mp0)
REVERT: A  959 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7339 (ttm170)
REVERT: A 1070 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7945 (pm20)
REVERT: A 1320 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7556 (m)
REVERT: A 1340 LYS cc_start: 0.8438 (mttm) cc_final: 0.7738 (tmmm)
  outliers start: 40
  outliers final: 19
  residues processed: 103
  average time/residue: 0.3895
  time to fit residues: 43.0601
Evaluate side-chains
  96 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 70
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  564 ASN
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  824 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  959 ARG
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1070 GLU
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1302 LEU
Chi-restraints excluded: chain A residue 1320 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 42 optimal weight:   20.0000
   chunk 1 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 282 HIS
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 956 HIS
A1214 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.178435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.110061 restraints weight = 9387.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.42
r_work: 0.3047 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   8548  Z= 0.246
  Angle     :  0.636   9.158  11613  Z= 0.309
  Chirality :  0.043   0.171   1368
  Planarity :  0.005   0.043   1440
  Dihedral  :  6.984  73.794   1240
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 19.42 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.62 (0.27), residues: 1030
  helix:  2.22 (0.22), residues: 566
  sheet: -1.01 (0.44), residues: 114
  loop : -0.04 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1254 
 TYR   0.017   0.001   TYR A 312 
 PHE   0.023   0.002   PHE A 823 
 TRP   0.010   0.002   TRP A 310 
 HIS   0.004   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00618 ( 8544)
  covalent geometry    : angle       0.63143 (11601)
  hydrogen bonds       : bond        0.06226 (  470)
  hydrogen bonds       : angle       4.32294 ( 1389)
  link_BETA1-4         : bond        0.00016 (    2)
  link_BETA1-4         : angle       2.26048 (    6)
  link_NAG-ASN         : bond        0.00623 (    2)
  link_NAG-ASN         : angle       2.52769 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 71
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.7841 (tp30) cc_final: 0.7605 (tp30)
REVERT: A  118 ARG cc_start: 0.7311 (ttm170) cc_final: 0.6750 (ttm-80)
REVERT: A  122 ARG cc_start: 0.8138 (mtm180) cc_final: 0.7835 (mtt180)
REVERT: A  404 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8288 (tp)
REVERT: A  433 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6172 (pp)
REVERT: A  555 MET cc_start: 0.3802 (mmp) cc_final: 0.3426 (mmm)
REVERT: A  602 LEU cc_start: -0.0477 (OUTLIER) cc_final: -0.1068 (mt)
REVERT: A  700 MET cc_start: 0.0377 (ptt) cc_final: -0.0852 (ttt)
REVERT: A  781 MET cc_start: 0.0187 (ppp) cc_final: -0.0184 (ptp)
REVERT: A  830 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7247 (mm110)
REVERT: A  872 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7643 (mp0)
REVERT: A  875 TRP cc_start: 0.7943 (OUTLIER) cc_final: 0.7661 (p-90)
REVERT: A  959 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7437 (ttm170)
REVERT: A 1011 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8488 (tt)
REVERT: A 1340 LYS cc_start: 0.8623 (mttm) cc_final: 0.7965 (tmmm)
  outliers start: 43
  outliers final: 25
  residues processed: 103
  average time/residue: 0.4133
  time to fit residues: 45.5239
Evaluate side-chains
  100 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 68
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  824 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  875 TRP
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  959 ARG
Chi-restraints excluded: chain A residue 1011 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1224 ASP
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1302 LEU
Chi-restraints excluded: chain A residue 1320 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9990
   chunk 47 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0070
   chunk 56 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
A 282 HIS
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 956 HIS
A1214 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.180366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.113429 restraints weight = 9403.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 3.10
r_work: 0.3063 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8548  Z= 0.140
  Angle     :  0.570   9.309  11613  Z= 0.278
  Chirality :  0.039   0.170   1368
  Planarity :  0.004   0.043   1440
  Dihedral  :  6.617  72.370   1240
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 20.17 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.80 (0.27), residues: 1030
  helix:  2.43 (0.22), residues: 562
  sheet: -0.99 (0.45), residues: 114
  loop : -0.02 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1068 
 TYR   0.014   0.001   TYR A 312 
 PHE   0.022   0.001   PHE A 823 
 TRP   0.011   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8544)
  covalent geometry    : angle       0.56552 (11601)
  hydrogen bonds       : bond        0.05319 (  470)
  hydrogen bonds       : angle       4.20117 ( 1389)
  link_BETA1-4         : bond        0.00185 (    2)
  link_BETA1-4         : angle       2.25525 (    6)
  link_NAG-ASN         : bond        0.00309 (    2)
  link_NAG-ASN         : angle       2.34254 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 72
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7339 (ttm170) cc_final: 0.6776 (ttm-80)
REVERT: A  122 ARG cc_start: 0.8128 (mtm180) cc_final: 0.7858 (mtt180)
REVERT: A  140 ARG cc_start: 0.7614 (ttp-110) cc_final: 0.6753 (tpm170)
REVERT: A  404 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8187 (tp)
REVERT: A  433 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6123 (pp)
REVERT: A  555 MET cc_start: 0.3802 (mmp) cc_final: 0.3393 (mmm)
REVERT: A  602 LEU cc_start: -0.0473 (OUTLIER) cc_final: -0.1066 (mt)
REVERT: A  700 MET cc_start: 0.0494 (ptt) cc_final: -0.0339 (ttt)
REVERT: A  754 MET cc_start: 0.0867 (mmm) cc_final: -0.0609 (tpp)
REVERT: A  830 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7253 (mm110)
REVERT: A  872 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7622 (mp0)
REVERT: A  875 TRP cc_start: 0.7895 (t60) cc_final: 0.7625 (p-90)
REVERT: A  959 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7420 (ttm170)
REVERT: A 1340 LYS cc_start: 0.8539 (mttm) cc_final: 0.7881 (tmmm)
  outliers start: 38
  outliers final: 22
  residues processed: 104
  average time/residue: 0.3732
  time to fit residues: 41.8283
Evaluate side-chains
  95 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  564 ASN
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  824 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  959 ARG
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1302 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:   30.0000
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 87 optimal weight:    0.7980
   chunk 29 optimal weight:    0.2980
   chunk 74 optimal weight:    0.6980
   chunk 66 optimal weight:    0.4980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 282 HIS
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 956 HIS
A1214 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.181204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113897 restraints weight = 9350.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.36
r_work: 0.3075 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8548  Z= 0.126
  Angle     :  0.549   9.329  11613  Z= 0.268
  Chirality :  0.038   0.171   1368
  Planarity :  0.004   0.042   1440
  Dihedral  :  6.428  72.917   1240
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.70 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.93 (0.27), residues: 1030
  helix:  2.56 (0.22), residues: 561
  sheet: -0.93 (0.45), residues: 114
  loop :  0.01 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1254 
 TYR   0.013   0.001   TYR A 312 
 PHE   0.019   0.001   PHE A 823 
 TRP   0.011   0.001   TRP A 310 
 HIS   0.002   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8544)
  covalent geometry    : angle       0.54449 (11601)
  hydrogen bonds       : bond        0.04988 (  470)
  hydrogen bonds       : angle       4.12137 ( 1389)
  link_BETA1-4         : bond        0.00253 (    2)
  link_BETA1-4         : angle       2.23427 (    6)
  link_NAG-ASN         : bond        0.00217 (    2)
  link_NAG-ASN         : angle       2.28459 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 70
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7395 (ttm170) cc_final: 0.6779 (ttm-80)
REVERT: A  122 ARG cc_start: 0.8119 (mtm180) cc_final: 0.7865 (mtt180)
REVERT: A  140 ARG cc_start: 0.7555 (ttp-110) cc_final: 0.6723 (tpm170)
REVERT: A  404 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8115 (tp)
REVERT: A  433 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6275 (pp)
REVERT: A  555 MET cc_start: 0.3791 (mmp) cc_final: 0.3367 (mmm)
REVERT: A  602 LEU cc_start: -0.0463 (OUTLIER) cc_final: -0.1065 (mt)
REVERT: A  700 MET cc_start: 0.0490 (ptt) cc_final: -0.0366 (ttt)
REVERT: A  754 MET cc_start: 0.0905 (mmm) cc_final: -0.0553 (tpp)
REVERT: A  830 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7209 (mm110)
REVERT: A  872 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7627 (mp0)
REVERT: A  875 TRP cc_start: 0.7872 (t60) cc_final: 0.7625 (p-90)
REVERT: A  959 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7451 (ttm170)
REVERT: A 1340 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7866 (tmmm)
  outliers start: 32
  outliers final: 24
  residues processed: 95
  average time/residue: 0.4290
  time to fit residues: 43.7739
Evaluate side-chains
  97 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  564 ASN
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  824 MET
Chi-restraints excluded: chain A residue  842 ASP
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  959 ARG
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1302 LEU
Chi-restraints excluded: chain A residue 1340 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 83 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 282 HIS
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 956 HIS
A1214 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.181777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.113172 restraints weight = 9440.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 3.25
r_work: 0.3086 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8548  Z= 0.138
  Angle     :  0.557   9.292  11613  Z= 0.272
  Chirality :  0.039   0.172   1368
  Planarity :  0.004   0.043   1440
  Dihedral  :  6.386  73.198   1240
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.96 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.94 (0.27), residues: 1030
  helix:  2.56 (0.22), residues: 561
  sheet: -0.88 (0.46), residues: 114
  loop :  0.01 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1254 
 TYR   0.013   0.001   TYR A 312 
 PHE   0.018   0.001   PHE A 823 
 TRP   0.010   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8544)
  covalent geometry    : angle       0.55218 (11601)
  hydrogen bonds       : bond        0.05089 (  470)
  hydrogen bonds       : angle       4.10475 ( 1389)
  link_BETA1-4         : bond        0.00214 (    2)
  link_BETA1-4         : angle       2.20140 (    6)
  link_NAG-ASN         : bond        0.00223 (    2)
  link_NAG-ASN         : angle       2.26406 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 68
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.7656 (tp30) cc_final: 0.7405 (tp30)
REVERT: A  118 ARG cc_start: 0.7350 (ttm170) cc_final: 0.6730 (ttm-80)
REVERT: A  122 ARG cc_start: 0.8060 (mtm180) cc_final: 0.7799 (mtt180)
REVERT: A  140 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.6771 (tpm170)
REVERT: A  404 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8071 (tp)
REVERT: A  433 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6314 (pp)
REVERT: A  555 MET cc_start: 0.3705 (mmp) cc_final: 0.3281 (mmm)
REVERT: A  602 LEU cc_start: -0.0641 (OUTLIER) cc_final: -0.1146 (mt)
REVERT: A  700 MET cc_start: 0.0794 (ptt) cc_final: -0.0739 (ttt)
REVERT: A  830 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7246 (mm-40)
REVERT: A  872 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7596 (mp0)
REVERT: A  875 TRP cc_start: 0.7834 (t60) cc_final: 0.7592 (p-90)
REVERT: A  959 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7432 (ttm170)
REVERT: A 1011 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8368 (tt)
REVERT: A 1340 LYS cc_start: 0.8464 (mttm) cc_final: 0.7817 (tmmm)
REVERT: A 1345 GLN cc_start: 0.8177 (tt0) cc_final: 0.7954 (tt0)
  outliers start: 39
  outliers final: 24
  residues processed: 96
  average time/residue: 0.4035
  time to fit residues: 41.8099
Evaluate side-chains
  95 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 65
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  564 ASN
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  824 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  959 ARG
Chi-restraints excluded: chain A residue 1011 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1151 MET
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1302 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
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: 63.209 > 50:
  distance: 101 - 105:  17.367
  distance: 105 - 106:  28.113
  distance: 106 - 107:  35.287
  distance: 106 - 109:  39.468
  distance: 107 - 108:  44.508
  distance: 107 - 113:  36.131
  distance: 109 - 110:  37.546
  distance: 109 - 111:  34.020
  distance: 110 - 112:  24.972
  distance: 113 - 114:  46.767
  distance: 113 - 213:  37.156
  distance: 114 - 115:  48.265
  distance: 114 - 117:  12.339
  distance: 115 - 116:  50.778
  distance: 115 - 118:  47.962
  distance: 116 - 224:  28.982
  distance: 118 - 119:  27.159
  distance: 119 - 120:  39.290
  distance: 119 - 122:  22.979
  distance: 120 - 121:  28.138
  distance: 120 - 126:  33.935
  distance: 122 - 123:  12.888
  distance: 123 - 124:  21.495
  distance: 123 - 125:  21.233
  distance: 126 - 127:  39.933
  distance: 127 - 128:  60.280
  distance: 127 - 130:  47.020
  distance: 128 - 129:   8.338
  distance: 128 - 134:  56.610
  distance: 130 - 131:  46.457
  distance: 131 - 132:  63.209
  distance: 131 - 133:  42.214
  distance: 134 - 135:  51.355
  distance: 134 - 140:  12.723
  distance: 135 - 136:  42.448
  distance: 135 - 138:  19.642
  distance: 136 - 137:  43.228
  distance: 136 - 141:  18.065
  distance: 138 - 139:  27.588
  distance: 139 - 140:  57.508
  distance: 141 - 142:  43.188
  distance: 142 - 143:  47.365
  distance: 142 - 145:  23.287
  distance: 143 - 144:  57.930
  distance: 145 - 146:  10.576
  distance: 146 - 147:  17.481
  distance: 146 - 148:  17.158
  distance: 149 - 150:   3.966
  distance: 150 - 151:  42.926
  distance: 150 - 153:  42.970
  distance: 151 - 152:  38.961
  distance: 151 - 161:  22.054
  distance: 153 - 154:  47.059
  distance: 154 - 155:  24.272
  distance: 154 - 156:  11.062
  distance: 155 - 157:  23.067
  distance: 156 - 158:  39.847
  distance: 157 - 159:  19.358
  distance: 158 - 159:  16.980
  distance: 159 - 160:   7.890
  distance: 161 - 162:  31.993
  distance: 161 - 167:  32.442
  distance: 162 - 163:  55.355
  distance: 162 - 165:  61.149
  distance: 163 - 164:  46.237
  distance: 163 - 168:  50.742
  distance: 165 - 166:  38.635
  distance: 166 - 167:  35.819
  distance: 168 - 169:  25.517
  distance: 169 - 170:   7.546
  distance: 169 - 172:   8.435
  distance: 170 - 171:   4.228
  distance: 172 - 173:  20.711
  distance: 174 - 175:  31.336
  distance: 175 - 176:  19.451
  distance: 175 - 178:  33.738
  distance: 176 - 177:  57.197
  distance: 176 - 182:  32.539
  distance: 178 - 179:   9.377
  distance: 179 - 180:  31.149
  distance: 179 - 181:   9.488