Starting phenix.real_space_refine
on Sat Aug 23 03:31:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fg2_31574/08_2025/7fg2_31574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fg2_31574/08_2025/7fg2_31574.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fg2_31574/08_2025/7fg2_31574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fg2_31574/08_2025/7fg2_31574.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fg2_31574/08_2025/7fg2_31574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fg2_31574/08_2025/7fg2_31574.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    5932      2.51       5
     N    1574      2.21       5
     O    1795      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 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: 9342
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8468
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1086, 8468
          Classifications: {'peptide': 1086}
          Link IDs: {'PTRANS': 50, 'TRANS': 1035}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 874
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 2, 'TRANS': 113}
  Time building chain proxies: 1.79, per 1000 atoms: 0.19
  Number of scatterers: 9342
  At special positions: 0
  Unit cell: (92.43, 139.356, 182.016, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1795      8.00
     N    1574      7.00
     C    5932      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 743 " - pdb=" SG  CYS A 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1032 " - pdb=" SG  CYS A1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  97 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 222.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2228

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 19 sheets defined
      21.6% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 184
      removed outlier: 3.839A  pdb=" N   GLY A 184 " --> pdb=" O   GLU A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 303
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.704A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 4.458A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.119A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 737 through 743
    Processing helix  chain 'A' and resid 746 through 756
    Processing helix  chain 'A' and resid 758 through 783
    Processing helix  chain 'A' and resid 811 through 815
      removed outlier: 4.060A  pdb=" N   ARG A 815 " --> pdb=" O   PRO A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 826
      removed outlier: 3.627A  pdb=" N   VAL A 826 " --> pdb=" O   LEU A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 883
    Processing helix  chain 'A' and resid 897 through 907
      removed outlier: 3.965A  pdb=" N   ARG A 905 " --> pdb=" O   GLN A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 941
      removed outlier: 4.221A  pdb=" N   LEU A 916 " --> pdb=" O   THR A 912 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR A 917 " --> pdb=" O   GLN A 913 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   LYS A 921 " --> pdb=" O   TYR A 917 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU A 922 " --> pdb=" O   GLU A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 967
      removed outlier: 3.766A  pdb=" N   GLN A 949 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 976 through 984
      removed outlier: 4.245A  pdb=" N   ILE A 980 " --> pdb=" O   VAL A 976 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LEU A 984 " --> pdb=" O   ILE A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 1034
    Processing helix  chain 'D' and resid 88 through 92
      removed outlier: 3.605A  pdb=" N   ASP D  91 " --> pdb=" O   LYS D  88 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   THR D  92 " --> pdb=" O   PRO D  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 88 through 92'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
      removed outlier: 3.847A  pdb=" N   SER A  60 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55
      removed outlier: 3.850A  pdb=" N   ASP A  53 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG A 273 " --> pdb=" O   ASP A  53 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A 276 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   ALA A 288 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LYS A 278 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.561A  pdb=" N   VAL A 120 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL A 127 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 227
      removed outlier: 3.981A  pdb=" N   GLU A 224 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TYR A 204 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   VAL A 193 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA A  93 " --> pdb=" O   TYR A 266 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   THR A  95 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ALA A 264 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 189
    Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358
    Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 380
      removed outlier: 4.682A  pdb=" N   GLY A 431 " --> pdb=" O   TYR A 380 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454
      removed outlier: 4.365A  pdb=" N   ASN A 450 " --> pdb=" O   TYR A 495 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   TYR A 495 " --> pdb=" O   ASN A 450 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   LEU A 452 " --> pdb=" O   GLN A 493 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   GLN A 493 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543
    Processing sheet with id=AB2, first strand: chain 'A' and resid 643 through 645
      removed outlier: 3.518A  pdb=" N   GLY A 648 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 713 through 722
      removed outlier: 6.882A  pdb=" N   ALA A 713 " --> pdb=" O   ASN A1074 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ASN A1074 " --> pdb=" O   ALA A 713 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLU A1072 " --> pdb=" O   PRO A 715 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ASN A 717 " --> pdb=" O   ALA A1070 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL A1065 " --> pdb=" O   LEU A1049 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR A1047 " --> pdb=" O   TYR A1067 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 728
    Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736
      removed outlier: 3.548A  pdb=" N   SER A 735 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1076 through 1077
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1089 through 1090
    Processing sheet with id=AB8, first strand: chain 'D' and resid 6 through 8
      removed outlier: 4.263A  pdb=" N   CYS D  23 " --> pdb=" O   VAL D  80 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL D  80 " --> pdb=" O   CYS D  23 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 36 through 40
      removed outlier: 8.124A  pdb=" N   TRP D  37 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   VAL D  49 " --> pdb=" O   TRP D  37 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 95

    278 hydrogen bonds defined for protein.
    741 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: 1.50

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3002
        1.34 -     1.46: 1876
        1.46 -     1.58: 4622
        1.58 -     1.69: 0
        1.69 -     1.81: 53
  Bond restraints: 9553
  Sorted by residual:
  bond pdb=" CA  TYR A 612 "
       pdb=" CB  TYR A 612 "
    ideal  model  delta    sigma   weight residual
    1.528  1.484  0.043 1.39e-02 5.18e+03 9.79e+00
  bond pdb=" C   ILE A 726 "
       pdb=" N   LEU A 727 "
    ideal  model  delta    sigma   weight residual
    1.331  1.291  0.040 1.36e-02 5.41e+03 8.50e+00
  bond pdb=" CB  VAL A 687 "
       pdb=" CG1 VAL A 687 "
    ideal  model  delta    sigma   weight residual
    1.521  1.433  0.088 3.30e-02 9.18e+02 7.12e+00
  bond pdb=" CA  SER A 982 "
       pdb=" C   SER A 982 "
    ideal  model  delta    sigma   weight residual
    1.523  1.485  0.038 1.48e-02 4.57e+03 6.70e+00
  bond pdb=" CB  THR A 299 "
       pdb=" CG2 THR A 299 "
    ideal  model  delta    sigma   weight residual
    1.521  1.450  0.071 3.30e-02 9.18e+02 4.65e+00
  ... (remaining 9548 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 11989
        1.97 -     3.93: 837
        3.93 -     5.90: 129
        5.90 -     7.86: 28
        7.86 -     9.82: 9
  Bond angle restraints: 12992
  Sorted by residual:
  angle pdb=" N   VAL A 483 "
        pdb=" CA  VAL A 483 "
        pdb=" C   VAL A 483 "
      ideal   model   delta    sigma   weight residual
     113.71  106.29    7.42 9.50e-01 1.11e+00 6.10e+01
  angle pdb=" N   SER A 325 "
        pdb=" CA  SER A 325 "
        pdb=" C   SER A 325 "
      ideal   model   delta    sigma   weight residual
     107.73  116.63   -8.90 1.34e+00 5.57e-01 4.41e+01
  angle pdb=" C   LEU A 176 "
        pdb=" N   MET A 177 "
        pdb=" CA  MET A 177 "
      ideal   model   delta    sigma   weight residual
     121.54  131.36   -9.82 1.91e+00 2.74e-01 2.65e+01
  angle pdb=" C   MET A 177 "
        pdb=" N   ASP A 178 "
        pdb=" CA  ASP A 178 "
      ideal   model   delta    sigma   weight residual
     121.54  131.32   -9.78 1.91e+00 2.74e-01 2.62e+01
  angle pdb=" N   SER A 591 "
        pdb=" CA  SER A 591 "
        pdb=" CB  SER A 591 "
      ideal   model   delta    sigma   weight residual
     114.17  108.42    5.75 1.14e+00 7.69e-01 2.54e+01
  ... (remaining 12987 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5144
       17.97 -    35.94: 418
       35.94 -    53.92: 67
       53.92 -    71.89: 17
       71.89 -    89.86: 14
  Dihedral angle restraints: 5660
    sinusoidal: 2182
      harmonic: 3478
  Sorted by residual:
  dihedral pdb=" CA  ASP A 178 "
           pdb=" C   ASP A 178 "
           pdb=" N   LEU A 179 "
           pdb=" CA  LEU A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -119.39  -60.61     0      5.00e+00 4.00e-02 1.47e+02
  dihedral pdb=" CA  SER A 591 "
           pdb=" C   SER A 591 "
           pdb=" N   PHE A 592 "
           pdb=" CA  PHE A 592 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  125.20   54.80     0      5.00e+00 4.00e-02 1.20e+02
  dihedral pdb=" CA  ALA A 623 "
           pdb=" C   ALA A 623 "
           pdb=" N   ILE A 624 "
           pdb=" CA  ILE A 624 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -125.21  -54.79     0      5.00e+00 4.00e-02 1.20e+02
  ... (remaining 5657 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 959
       0.043 -    0.086: 340
       0.086 -    0.129: 132
       0.129 -    0.173: 26
       0.173 -    0.216: 8
  Chirality restraints: 1465
  Sorted by residual:
  chirality pdb=" CB  THR A 274 "
            pdb=" CA  THR A 274 "
            pdb=" OG1 THR A 274 "
            pdb=" CG2 THR A 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  THR A 827 "
            pdb=" CA  THR A 827 "
            pdb=" OG1 THR A 827 "
            pdb=" CG2 THR A 827 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  VAL A 705 "
            pdb=" N   VAL A 705 "
            pdb=" C   VAL A 705 "
            pdb=" CB  VAL A 705 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1462 not shown)

  Planarity restraints: 1689
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 599 "   -0.050 5.00e-02 4.00e+02   7.71e-02 9.51e+00
        pdb=" N   PRO A 600 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 600 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 600 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 714 "    0.051 5.00e-02 4.00e+02   7.67e-02 9.41e+00
        pdb=" N   PRO A 715 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 715 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 715 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 321 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.61e+00
        pdb=" N   PRO A 322 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1686 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 253
        2.62 -     3.19: 9728
        3.19 -     3.76: 14685
        3.76 -     4.33: 20347
        4.33 -     4.90: 31549
  Nonbonded interactions: 76562
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 880 "
            pdb=" OG  SER A 884 "
     model   vdw
     2.053 3.040
  nonbonded pdb=" O   GLU A 661 "
            pdb=" OH  TYR A 695 "
     model   vdw
     2.058 3.040
  nonbonded pdb=" OD1 ASN A 709 "
            pdb=" N   ASN A 710 "
     model   vdw
     2.058 3.120
  nonbonded pdb=" OG1 THR A 478 "
            pdb=" OD1 ASN A 481 "
     model   vdw
     2.061 3.040
  nonbonded pdb=" OG  SER D  18 "
            pdb=" OD1 ASN D  85 "
     model   vdw
     2.091 3.040
  ... (remaining 76557 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.180
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6570
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      :  0.007   0.088   9562  Z= 0.338
  Angle     :  1.136   9.825  13010  Z= 0.679
  Chirality :  0.053   0.216   1465
  Planarity :  0.006   0.077   1689
  Dihedral  : 14.434  89.862   3405
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 32.59
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 17.84 %
    Favored  : 81.74 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.19 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.70 %

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: -3.95 (0.22), residues: 1194
  helix: -0.70 (0.34), residues: 222
  sheet: -2.12 (0.34), residues: 217
  loop : -3.63 (0.19), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 319 
 TYR   0.027   0.003   TYR A 789 
 PHE   0.028   0.003   PHE A 797 
 TRP   0.021   0.003   TRP A1102 
 HIS   0.006   0.002   HIS A1083 

Details of bonding type rmsd
  covalent geometry    : bond        0.00687 ( 9553)
  covalent geometry    : angle       1.13435 (12992)
  SS BOND              : bond        0.00718 (    9)
  SS BOND              : angle       1.80643 (   18)
  hydrogen bonds       : bond        0.23086 (  278)
  hydrogen bonds       : angle       9.47396 (  741)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 222
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 SER cc_start: 0.7650 (t) cc_final: 0.7377 (t)
REVERT: A  137 ASN cc_start: 0.6800 (p0) cc_final: 0.6321 (p0)
REVERT: A  223 LEU cc_start: 0.8221 (mp) cc_final: 0.8019 (mp)
REVERT: A  350 VAL cc_start: 0.8770 (p) cc_final: 0.7999 (p)
REVERT: A  400 PHE cc_start: 0.8231 (p90) cc_final: 0.7715 (p90)
REVERT: A  559 PHE cc_start: 0.7741 (m-10) cc_final: 0.7466 (m-10)
REVERT: A  738 CYS cc_start: 0.9078 (t) cc_final: 0.8692 (t)
REVERT: A  818 ILE cc_start: 0.7786 (mt) cc_final: 0.6826 (mt)
REVERT: A  900 MET cc_start: 0.7036 (mpp) cc_final: 0.6521 (mpp)
REVERT: A 1010 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8270 (tp-100)
REVERT: D   71 ILE cc_start: 0.3741 (tp) cc_final: 0.3287 (tp)
REVERT: D   84 MET cc_start: 0.5086 (pmm) cc_final: 0.4705 (pmm)
  outliers start: 2
  outliers final: 0
  residues processed: 222
  average time/residue: 0.0788
  time to fit residues: 24.6727
Evaluate side-chains
  167 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 117 optimal weight:    0.0970
   overall best weight:    1.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 211 ASN
A 343 ASN
A 448 ASN
A 606 ASN
A 777 ASN
A 824 ASN
** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 928 ASN
A 935 GLN
A1005 GLN
** D  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.177932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.148378 restraints weight = 26623.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.150504 restraints weight = 17990.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.151501 restraints weight = 13520.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.152963 restraints weight = 11365.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.153542 restraints weight = 9742.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9562  Z= 0.180
  Angle     :  0.797  10.412  13010  Z= 0.432
  Chirality :  0.049   0.214   1465
  Planarity :  0.006   0.067   1689
  Dihedral  :  7.593  64.651   1296
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 17.89
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 14.41 %
    Favored  : 85.18 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  5.79 %
    Favored  : 93.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.61 %

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: -3.45 (0.23), residues: 1194
  helix:  0.13 (0.35), residues: 221
  sheet: -1.89 (0.34), residues: 208
  loop : -3.39 (0.20), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 905 
 TYR   0.021   0.002   TYR A 451 
 PHE   0.025   0.002   PHE A1121 
 TRP   0.011   0.002   TRP A 436 
 HIS   0.006   0.001   HIS A 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 9553)
  covalent geometry    : angle       0.79615 (12992)
  SS BOND              : bond        0.00477 (    9)
  SS BOND              : angle       1.32328 (   18)
  hydrogen bonds       : bond        0.05727 (  278)
  hydrogen bonds       : angle       7.22804 (  741)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 227
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 THR cc_start: 0.8022 (t) cc_final: 0.7789 (m)
REVERT: A   52 GLN cc_start: 0.8173 (pp30) cc_final: 0.7498 (pp30)
REVERT: A  137 ASN cc_start: 0.5683 (p0) cc_final: 0.5201 (p0)
REVERT: A  221 SER cc_start: 0.7627 (t) cc_final: 0.7397 (m)
REVERT: A  350 VAL cc_start: 0.8272 (p) cc_final: 0.7741 (p)
REVERT: A  400 PHE cc_start: 0.8093 (p90) cc_final: 0.7774 (p90)
REVERT: A  619 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6370 (mm-30)
REVERT: A  729 VAL cc_start: 0.8154 (t) cc_final: 0.7878 (p)
REVERT: A  773 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6863 (tm-30)
REVERT: A  777 ASN cc_start: 0.8550 (m110) cc_final: 0.8136 (m110)
REVERT: A  821 LEU cc_start: 0.8802 (tt) cc_final: 0.8546 (tt)
REVERT: A  900 MET cc_start: 0.6795 (mpp) cc_final: 0.6393 (mpp)
REVERT: A  933 LYS cc_start: 0.8907 (tttm) cc_final: 0.8409 (tttt)
REVERT: A 1005 GLN cc_start: 0.8687 (tp40) cc_final: 0.8440 (tp40)
REVERT: A 1010 GLN cc_start: 0.8405 (tp-100) cc_final: 0.7980 (tp-100)
REVERT: A 1028 LYS cc_start: 0.6561 (tptt) cc_final: 0.6214 (tptt)
REVERT: D   71 ILE cc_start: 0.3079 (tp) cc_final: 0.2691 (tp)
  outliers start: 4
  outliers final: 1
  residues processed: 228
  average time/residue: 0.0770
  time to fit residues: 25.0374
Evaluate side-chains
  180 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 91 optimal weight:    0.0870
   chunk 29 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 106 optimal weight:   20.0000
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.8166

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

Flipped N/Q/H residues before XYZ refinement:
** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 GLN
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 GLN
D  83 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.179471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.149485 restraints weight = 26111.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.151777 restraints weight = 16973.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.153529 restraints weight = 12491.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.154693 restraints weight = 9891.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.155284 restraints weight = 8434.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6418
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9562  Z= 0.169
  Angle     :  0.759  10.483  13010  Z= 0.407
  Chirality :  0.048   0.184   1465
  Planarity :  0.005   0.063   1689
  Dihedral  :  7.206  64.325   1296
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 15.33 %
    Favored  : 84.25 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  5.60 %
    Favored  : 94.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.44 %

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: -3.34 (0.23), residues: 1194
  helix:  0.40 (0.35), residues: 221
  sheet: -1.92 (0.35), residues: 190
  loop : -3.33 (0.20), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 190 
 TYR   0.019   0.002   TYR A 660 
 PHE   0.022   0.002   PHE A 592 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.006   0.001   HIS A 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9553)
  covalent geometry    : angle       0.75781 (12992)
  SS BOND              : bond        0.00557 (    9)
  SS BOND              : angle       1.21030 (   18)
  hydrogen bonds       : bond        0.04904 (  278)
  hydrogen bonds       : angle       6.51950 (  741)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 220
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8108 (pp30) cc_final: 0.7785 (pp30)
REVERT: A  220 PHE cc_start: 0.7128 (t80) cc_final: 0.6579 (t80)
REVERT: A  221 SER cc_start: 0.7605 (t) cc_final: 0.7398 (m)
REVERT: A  274 THR cc_start: 0.7863 (t) cc_final: 0.7482 (t)
REVERT: A  350 VAL cc_start: 0.8348 (p) cc_final: 0.7262 (p)
REVERT: A  400 PHE cc_start: 0.7983 (p90) cc_final: 0.7501 (p90)
REVERT: A  697 MET cc_start: 0.7837 (tmm) cc_final: 0.7532 (tmm)
REVERT: A  732 THR cc_start: 0.8745 (p) cc_final: 0.8515 (p)
REVERT: A  738 CYS cc_start: 0.8511 (t) cc_final: 0.8208 (t)
REVERT: A  773 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6627 (tm-30)
REVERT: A  777 ASN cc_start: 0.8562 (m110) cc_final: 0.8084 (m110)
REVERT: A  818 ILE cc_start: 0.7843 (mt) cc_final: 0.7578 (mt)
REVERT: A  900 MET cc_start: 0.7041 (mpp) cc_final: 0.6716 (mpp)
REVERT: A  985 ASP cc_start: 0.7778 (m-30) cc_final: 0.7477 (m-30)
REVERT: A 1005 GLN cc_start: 0.8738 (tp40) cc_final: 0.8532 (tp40)
REVERT: A 1010 GLN cc_start: 0.8471 (tp-100) cc_final: 0.7978 (tp40)
REVERT: A 1028 LYS cc_start: 0.6568 (tptt) cc_final: 0.5685 (ttpt)
REVERT: A 1052 PHE cc_start: 0.7894 (m-10) cc_final: 0.7588 (m-10)
REVERT: D   33 TYR cc_start: 0.6099 (m-80) cc_final: 0.5708 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 222
  average time/residue: 0.0937
  time to fit residues: 29.3871
Evaluate side-chains
  178 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 81 optimal weight:    1.9990
   chunk 114 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 116 optimal weight:    0.6980
   chunk 37 optimal weight:   20.0000
   chunk 34 optimal weight:    9.9990
   chunk 98 optimal weight:    0.9990
   chunk 101 optimal weight:    0.0040
   overall best weight:    1.3398

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

Flipped N/Q/H residues before XYZ refinement:
** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.181528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.151382 restraints weight = 25962.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.153883 restraints weight = 16668.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.155616 restraints weight = 11926.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.156570 restraints weight = 9410.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.156817 restraints weight = 8105.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6387
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9562  Z= 0.148
  Angle     :  0.715   9.344  13010  Z= 0.383
  Chirality :  0.047   0.171   1465
  Planarity :  0.005   0.057   1689
  Dihedral  :  6.926  65.533   1296
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 14.07 %
    Favored  : 85.51 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.44 %
    Favored  : 95.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.35 %

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: -3.15 (0.23), residues: 1194
  helix:  0.50 (0.35), residues: 219
  sheet: -1.77 (0.35), residues: 194
  loop : -3.19 (0.20), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 190 
 TYR   0.018   0.001   TYR D  98 
 PHE   0.022   0.002   PHE A 592 
 TRP   0.011   0.002   TRP D  37 
 HIS   0.004   0.001   HIS A 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9553)
  covalent geometry    : angle       0.71249 (12992)
  SS BOND              : bond        0.00439 (    9)
  SS BOND              : angle       1.63680 (   18)
  hydrogen bonds       : bond        0.04571 (  278)
  hydrogen bonds       : angle       6.19831 (  741)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8058 (pp30) cc_final: 0.7644 (pp30)
REVERT: A   80 ASP cc_start: 0.8172 (p0) cc_final: 0.7927 (p0)
REVERT: A  221 SER cc_start: 0.7830 (t) cc_final: 0.7601 (m)
REVERT: A  350 VAL cc_start: 0.8367 (p) cc_final: 0.7260 (p)
REVERT: A  351 TYR cc_start: 0.6284 (t80) cc_final: 0.5961 (t80)
REVERT: A  400 PHE cc_start: 0.7925 (p90) cc_final: 0.7450 (p90)
REVERT: A  613 GLN cc_start: 0.7919 (mt0) cc_final: 0.7325 (pt0)
REVERT: A  640 SER cc_start: 0.7699 (p) cc_final: 0.7216 (t)
REVERT: A  773 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6037 (tm-30)
REVERT: A  777 ASN cc_start: 0.8572 (m110) cc_final: 0.7966 (m110)
REVERT: A  858 LEU cc_start: 0.8557 (mt) cc_final: 0.8193 (mt)
REVERT: A  859 THR cc_start: 0.8456 (t) cc_final: 0.8112 (m)
REVERT: A  900 MET cc_start: 0.7108 (mpp) cc_final: 0.6675 (mpp)
REVERT: A  935 GLN cc_start: 0.7729 (tp-100) cc_final: 0.6485 (tp-100)
REVERT: A  985 ASP cc_start: 0.7842 (m-30) cc_final: 0.7471 (m-30)
REVERT: A 1002 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7247 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8736 (tp40) cc_final: 0.8458 (tp40)
REVERT: A 1010 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8062 (tp40)
REVERT: A 1031 GLU cc_start: 0.6761 (mt-10) cc_final: 0.5985 (mt-10)
REVERT: D   33 TYR cc_start: 0.6133 (m-80) cc_final: 0.5851 (m-80)
REVERT: D   85 ASN cc_start: 0.6350 (m-40) cc_final: 0.5839 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0976
  time to fit residues: 29.6632
Evaluate side-chains
  176 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 38 optimal weight:    0.0030
   chunk 73 optimal weight:    0.9990
   chunk 81 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 86 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 61 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0570
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.5112

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.185096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.155095 restraints weight = 26143.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.157683 restraints weight = 16628.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.159504 restraints weight = 11825.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.160205 restraints weight = 9300.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.160541 restraints weight = 8148.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6301
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9562  Z= 0.128
  Angle     :  0.683   9.035  13010  Z= 0.366
  Chirality :  0.047   0.170   1465
  Planarity :  0.005   0.051   1689
  Dihedral  :  6.490  63.125   1296
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 12.65 %
    Favored  : 86.93 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.51 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.35 %

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: -2.93 (0.23), residues: 1194
  helix:  0.65 (0.36), residues: 217
  sheet: -1.50 (0.36), residues: 200
  loop : -3.07 (0.20), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 190 
 TYR   0.015   0.001   TYR A 421 
 PHE   0.021   0.001   PHE A 592 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9553)
  covalent geometry    : angle       0.68075 (12992)
  SS BOND              : bond        0.00533 (    9)
  SS BOND              : angle       1.52738 (   18)
  hydrogen bonds       : bond        0.04218 (  278)
  hydrogen bonds       : angle       5.80681 (  741)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 222
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7851 (pp30) cc_final: 0.7335 (pp30)
REVERT: A   80 ASP cc_start: 0.8136 (p0) cc_final: 0.7868 (p0)
REVERT: A  153 MET cc_start: 0.2706 (mtt) cc_final: 0.2101 (mtp)
REVERT: A  182 LYS cc_start: 0.6384 (mtmm) cc_final: 0.5750 (mmmt)
REVERT: A  350 VAL cc_start: 0.8395 (p) cc_final: 0.7243 (p)
REVERT: A  400 PHE cc_start: 0.7823 (p90) cc_final: 0.7403 (p90)
REVERT: A  553 THR cc_start: 0.6348 (m) cc_final: 0.6045 (m)
REVERT: A  613 GLN cc_start: 0.7747 (mt0) cc_final: 0.7229 (pt0)
REVERT: A  640 SER cc_start: 0.7475 (p) cc_final: 0.7103 (t)
REVERT: A  747 THR cc_start: 0.7384 (m) cc_final: 0.7015 (p)
REVERT: A  773 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6330 (tm-30)
REVERT: A  777 ASN cc_start: 0.8471 (m110) cc_final: 0.8139 (m110)
REVERT: A  985 ASP cc_start: 0.7728 (m-30) cc_final: 0.7410 (m-30)
REVERT: A 1002 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7465 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8625 (tp40) cc_final: 0.8422 (tp40)
REVERT: A 1010 GLN cc_start: 0.8364 (tp-100) cc_final: 0.8160 (tp40)
REVERT: A 1039 ARG cc_start: 0.6903 (ptp90) cc_final: 0.6681 (ptp90)
REVERT: A 1049 LEU cc_start: 0.6697 (mt) cc_final: 0.6374 (mp)
REVERT: A 1075 PHE cc_start: 0.6644 (m-10) cc_final: 0.6376 (m-10)
REVERT: D   33 TYR cc_start: 0.5635 (m-80) cc_final: 0.5327 (m-80)
REVERT: D   35 MET cc_start: -0.0053 (ptt) cc_final: -0.0276 (ptt)
REVERT: D   37 TRP cc_start: 0.0684 (m-90) cc_final: -0.0905 (m-90)
REVERT: D   85 ASN cc_start: 0.7012 (m-40) cc_final: 0.5716 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 222
  average time/residue: 0.0933
  time to fit residues: 29.1564
Evaluate side-chains
  185 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   chunk 107 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0000
   chunk 4 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 99 optimal weight:    0.0770
   chunk 31 optimal weight:   20.0000
   chunk 40 optimal weight:    0.0870
   chunk 100 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.4120

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.186421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.156137 restraints weight = 26217.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.158721 restraints weight = 16699.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.160518 restraints weight = 11940.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.161796 restraints weight = 9401.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.162278 restraints weight = 7898.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6242
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9562  Z= 0.124
  Angle     :  0.662   8.640  13010  Z= 0.353
  Chirality :  0.046   0.159   1465
  Planarity :  0.005   0.049   1689
  Dihedral  :  6.277  62.991   1296
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 12.48 %
    Favored  : 87.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.35 %

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: -2.81 (0.23), residues: 1194
  helix:  0.68 (0.35), residues: 217
  sheet: -1.24 (0.36), residues: 208
  loop : -3.03 (0.20), residues: 769

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 357 
 TYR   0.017   0.001   TYR A 660 
 PHE   0.026   0.002   PHE A 220 
 TRP   0.009   0.001   TRP A 258 
 HIS   0.003   0.001   HIS A 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9553)
  covalent geometry    : angle       0.65898 (12992)
  SS BOND              : bond        0.00490 (    9)
  SS BOND              : angle       1.79584 (   18)
  hydrogen bonds       : bond        0.03959 (  278)
  hydrogen bonds       : angle       5.68722 (  741)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7688 (pp30) cc_final: 0.7224 (pp30)
REVERT: A   80 ASP cc_start: 0.8094 (p0) cc_final: 0.7836 (p0)
REVERT: A  153 MET cc_start: 0.2543 (mtt) cc_final: 0.2142 (mtp)
REVERT: A  182 LYS cc_start: 0.6366 (mtmm) cc_final: 0.5894 (mmmt)
REVERT: A  220 PHE cc_start: 0.7428 (t80) cc_final: 0.7139 (t80)
REVERT: A  303 LEU cc_start: 0.8531 (tt) cc_final: 0.8328 (tt)
REVERT: A  350 VAL cc_start: 0.8321 (p) cc_final: 0.7156 (p)
REVERT: A  351 TYR cc_start: 0.6111 (t80) cc_final: 0.5800 (t80)
REVERT: A  400 PHE cc_start: 0.7721 (p90) cc_final: 0.7093 (p90)
REVERT: A  553 THR cc_start: 0.6300 (m) cc_final: 0.6019 (m)
REVERT: A  613 GLN cc_start: 0.7789 (mt0) cc_final: 0.7258 (pt0)
REVERT: A  640 SER cc_start: 0.7432 (p) cc_final: 0.7074 (t)
REVERT: A  732 THR cc_start: 0.8599 (p) cc_final: 0.8305 (p)
REVERT: A  747 THR cc_start: 0.7249 (m) cc_final: 0.6867 (p)
REVERT: A  773 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6281 (tm-30)
REVERT: A  777 ASN cc_start: 0.8438 (m110) cc_final: 0.8183 (m110)
REVERT: A  935 GLN cc_start: 0.7396 (tp-100) cc_final: 0.6373 (tp-100)
REVERT: A  959 LEU cc_start: 0.8775 (mp) cc_final: 0.8534 (mp)
REVERT: A  985 ASP cc_start: 0.7764 (m-30) cc_final: 0.7289 (m-30)
REVERT: A 1002 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7419 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8654 (tp40) cc_final: 0.8344 (tp40)
REVERT: A 1010 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8038 (tp40)
REVERT: A 1023 ASN cc_start: 0.7658 (m110) cc_final: 0.7426 (m110)
REVERT: A 1039 ARG cc_start: 0.6803 (ptp90) cc_final: 0.6379 (ptp90)
REVERT: A 1049 LEU cc_start: 0.6679 (mt) cc_final: 0.6218 (mp)
REVERT: A 1075 PHE cc_start: 0.6427 (m-10) cc_final: 0.5922 (m-10)
REVERT: D   33 TYR cc_start: 0.5553 (m-80) cc_final: 0.5348 (m-80)
REVERT: D   35 MET cc_start: 0.0151 (ptt) cc_final: -0.0277 (ptt)
REVERT: D   85 ASN cc_start: 0.7046 (m-40) cc_final: 0.5669 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.0914
  time to fit residues: 27.8260
Evaluate side-chains
  177 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 110 optimal weight:   20.0000
   chunk 103 optimal weight:    0.4980
   chunk 111 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9990
   chunk 109 optimal weight:   20.0000
   chunk 61 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0270
   overall best weight:    0.9042

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

Flipped N/Q/H residues before XYZ refinement:
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1058 HIS
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.185595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.155596 restraints weight = 26244.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.158295 restraints weight = 16615.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.160141 restraints weight = 11865.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.161194 restraints weight = 9264.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.162186 restraints weight = 7921.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6252
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9562  Z= 0.127
  Angle     :  0.660   8.818  13010  Z= 0.353
  Chirality :  0.046   0.163   1465
  Planarity :  0.004   0.040   1689
  Dihedral  :  6.183  60.901   1296
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.31 %
    Favored  : 87.35 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.32 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -2.83 (0.23), residues: 1194
  helix:  0.74 (0.36), residues: 216
  sheet: -1.34 (0.36), residues: 215
  loop : -3.05 (0.20), residues: 763

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1019 
 TYR   0.013   0.001   TYR A 453 
 PHE   0.027   0.002   PHE A 817 
 TRP   0.007   0.001   TRP D 107 
 HIS   0.002   0.001   HIS A 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9553)
  covalent geometry    : angle       0.65833 (12992)
  SS BOND              : bond        0.00606 (    9)
  SS BOND              : angle       1.44652 (   18)
  hydrogen bonds       : bond        0.04101 (  278)
  hydrogen bonds       : angle       5.64917 (  741)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 211
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7667 (pp30) cc_final: 0.7295 (pp30)
REVERT: A   80 ASP cc_start: 0.8076 (p0) cc_final: 0.7830 (p0)
REVERT: A  153 MET cc_start: 0.2840 (mtt) cc_final: 0.2185 (mtp)
REVERT: A  182 LYS cc_start: 0.6517 (mtmm) cc_final: 0.6094 (mmmt)
REVERT: A  220 PHE cc_start: 0.7450 (t80) cc_final: 0.7158 (t80)
REVERT: A  274 THR cc_start: 0.6503 (t) cc_final: 0.6298 (t)
REVERT: A  350 VAL cc_start: 0.8307 (p) cc_final: 0.7115 (p)
REVERT: A  400 PHE cc_start: 0.7682 (p90) cc_final: 0.7191 (p90)
REVERT: A  553 THR cc_start: 0.6385 (m) cc_final: 0.6125 (m)
REVERT: A  613 GLN cc_start: 0.8046 (mt0) cc_final: 0.7506 (pt0)
REVERT: A  747 THR cc_start: 0.7398 (m) cc_final: 0.7053 (p)
REVERT: A  777 ASN cc_start: 0.8185 (m110) cc_final: 0.7926 (m110)
REVERT: A  985 ASP cc_start: 0.7542 (m-30) cc_final: 0.7254 (m-30)
REVERT: A 1002 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7452 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8694 (tp40) cc_final: 0.8361 (tp40)
REVERT: A 1010 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8084 (tp40)
REVERT: A 1023 ASN cc_start: 0.7692 (m110) cc_final: 0.7435 (m110)
REVERT: A 1039 ARG cc_start: 0.6580 (ptp90) cc_final: 0.6133 (ptp90)
REVERT: A 1049 LEU cc_start: 0.6862 (mt) cc_final: 0.6244 (mp)
REVERT: A 1075 PHE cc_start: 0.5963 (m-10) cc_final: 0.4484 (m-10)
REVERT: D   85 ASN cc_start: 0.7100 (m-40) cc_final: 0.5622 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0888
  time to fit residues: 26.8164
Evaluate side-chains
  173 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 114 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 655 HIS
** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 955 ASN
** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1058 HIS
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.182466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152428 restraints weight = 26172.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.155100 restraints weight = 16341.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.156970 restraints weight = 11489.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.158218 restraints weight = 8920.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.158956 restraints weight = 7469.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6345
moved from start:          0.4538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9562  Z= 0.160
  Angle     :  0.711   8.934  13010  Z= 0.378
  Chirality :  0.047   0.170   1465
  Planarity :  0.005   0.042   1689
  Dihedral  :  6.373  60.626   1296
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.99 %
    Favored  : 85.76 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.54 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -2.89 (0.23), residues: 1194
  helix:  0.65 (0.36), residues: 216
  sheet: -1.60 (0.36), residues: 219
  loop : -2.99 (0.20), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1019 
 TYR   0.015   0.002   TYR A 904 
 PHE   0.026   0.002   PHE A1121 
 TRP   0.017   0.002   TRP D  37 
 HIS   0.009   0.001   HIS A 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9553)
  covalent geometry    : angle       0.70905 (12992)
  SS BOND              : bond        0.00614 (    9)
  SS BOND              : angle       1.66617 (   18)
  hydrogen bonds       : bond        0.04411 (  278)
  hydrogen bonds       : angle       5.90503 (  741)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 202
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.8103 (p0) cc_final: 0.7891 (p0)
REVERT: A  153 MET cc_start: 0.2874 (mtt) cc_final: 0.2279 (mtp)
REVERT: A  220 PHE cc_start: 0.7422 (t80) cc_final: 0.7058 (t80)
REVERT: A  350 VAL cc_start: 0.8454 (p) cc_final: 0.7321 (p)
REVERT: A  351 TYR cc_start: 0.6548 (t80) cc_final: 0.6096 (t80)
REVERT: A  374 PHE cc_start: 0.5628 (p90) cc_final: 0.4894 (p90)
REVERT: A  400 PHE cc_start: 0.7760 (p90) cc_final: 0.7379 (p90)
REVERT: A  553 THR cc_start: 0.6786 (m) cc_final: 0.6558 (m)
REVERT: A  613 GLN cc_start: 0.8147 (mt0) cc_final: 0.7518 (pt0)
REVERT: A  640 SER cc_start: 0.7475 (p) cc_final: 0.7112 (t)
REVERT: A  662 CYS cc_start: 0.5023 (p) cc_final: 0.4671 (p)
REVERT: A  747 THR cc_start: 0.7378 (m) cc_final: 0.7012 (p)
REVERT: A  773 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6748 (tm-30)
REVERT: A  777 ASN cc_start: 0.8370 (m110) cc_final: 0.7970 (m110)
REVERT: A  818 ILE cc_start: 0.8196 (mt) cc_final: 0.7586 (pt)
REVERT: A  935 GLN cc_start: 0.7113 (tp40) cc_final: 0.6729 (tp40)
REVERT: A  985 ASP cc_start: 0.7507 (m-30) cc_final: 0.7234 (m-30)
REVERT: A 1005 GLN cc_start: 0.8717 (tp40) cc_final: 0.8322 (tp-100)
REVERT: A 1010 GLN cc_start: 0.8629 (tp-100) cc_final: 0.7828 (tp40)
REVERT: A 1023 ASN cc_start: 0.7916 (m110) cc_final: 0.7617 (m110)
REVERT: A 1039 ARG cc_start: 0.6529 (ptp90) cc_final: 0.6012 (ptp90)
REVERT: A 1075 PHE cc_start: 0.5851 (m-10) cc_final: 0.4452 (m-10)
REVERT: A 1107 ARG cc_start: 0.7890 (mmp-170) cc_final: 0.7678 (mmm160)
REVERT: D   85 ASN cc_start: 0.7364 (m-40) cc_final: 0.5572 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 203
  average time/residue: 0.0894
  time to fit residues: 25.7621
Evaluate side-chains
  169 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 35 optimal weight:    9.9990
   chunk 111 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 655 HIS
A 926 GLN
** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  24 GLN
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.183244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.153096 restraints weight = 26195.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.155723 restraints weight = 16596.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.157563 restraints weight = 11778.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.158386 restraints weight = 9204.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.159487 restraints weight = 7955.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6324
moved from start:          0.4751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9562  Z= 0.142
  Angle     :  0.697   9.458  13010  Z= 0.368
  Chirality :  0.046   0.162   1465
  Planarity :  0.005   0.042   1689
  Dihedral  :  6.294  58.370   1296
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.57 %
    Favored  : 86.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -2.86 (0.23), residues: 1194
  helix:  0.57 (0.36), residues: 217
  sheet: -1.57 (0.35), residues: 220
  loop : -2.95 (0.20), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1019 
 TYR   0.015   0.001   TYR A 248 
 PHE   0.025   0.002   PHE A1121 
 TRP   0.008   0.001   TRP D 107 
 HIS   0.009   0.001   HIS A 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9553)
  covalent geometry    : angle       0.69458 (12992)
  SS BOND              : bond        0.00444 (    9)
  SS BOND              : angle       1.65019 (   18)
  hydrogen bonds       : bond        0.04186 (  278)
  hydrogen bonds       : angle       5.85158 (  741)

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

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

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2388 Ramachandran restraints generated.
    1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7999 (pp30) cc_final: 0.7668 (pp30)
REVERT: A  153 MET cc_start: 0.3041 (mtt) cc_final: 0.2355 (mtp)
REVERT: A  220 PHE cc_start: 0.7491 (t80) cc_final: 0.7097 (t80)
REVERT: A  350 VAL cc_start: 0.8440 (p) cc_final: 0.7280 (p)
REVERT: A  351 TYR cc_start: 0.6332 (t80) cc_final: 0.6002 (t80)
REVERT: A  374 PHE cc_start: 0.5552 (p90) cc_final: 0.4820 (p90)
REVERT: A  400 PHE cc_start: 0.7686 (p90) cc_final: 0.7323 (p90)
REVERT: A  553 THR cc_start: 0.6538 (m) cc_final: 0.6278 (m)
REVERT: A  613 GLN cc_start: 0.8121 (mt0) cc_final: 0.7378 (pt0)
REVERT: A  640 SER cc_start: 0.7433 (p) cc_final: 0.7078 (t)
REVERT: A  662 CYS cc_start: 0.5023 (p) cc_final: 0.4720 (p)
REVERT: A  747 THR cc_start: 0.7403 (m) cc_final: 0.7088 (p)
REVERT: A  773 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6640 (tm-30)
REVERT: A  777 ASN cc_start: 0.8332 (m110) cc_final: 0.7968 (m110)
REVERT: A  804 GLN cc_start: 0.6189 (mm-40) cc_final: 0.4872 (tp-100)
REVERT: A  934 ILE cc_start: 0.8387 (mt) cc_final: 0.8086 (mt)
REVERT: A  935 GLN cc_start: 0.7191 (tp40) cc_final: 0.6356 (tp40)
REVERT: A 1002 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7852 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8670 (tp40) cc_final: 0.8428 (tp40)
REVERT: A 1010 GLN cc_start: 0.8427 (tp-100) cc_final: 0.7907 (tp40)
REVERT: A 1039 ARG cc_start: 0.6493 (ptp90) cc_final: 0.6104 (ptp90)
REVERT: D   85 ASN cc_start: 0.7326 (m-40) cc_final: 0.5340 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0846
  time to fit residues: 23.6336
Evaluate side-chains
  172 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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: 67.0498 > 50:
  distance: 22 - 146:  14.071
  distance: 23 - 140:  18.122
  distance: 69 - 79:  27.427
  distance: 79 - 80:  16.976
  distance: 80 - 81:  53.381
  distance: 80 - 83:  15.606
  distance: 81 - 82:  28.662
  distance: 81 - 88:  52.155
  distance: 83 - 84:  21.205
  distance: 84 - 85:  26.863
  distance: 85 - 86:  15.536
  distance: 86 - 87:  13.144
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