Starting phenix.real_space_refine
on Thu Feb 13 22:12:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fg2_31574/02_2025/7fg2_31574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fg2_31574/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fg2_31574/02_2025/7fg2_31574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fg2_31574/02_2025/7fg2_31574.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fg2_31574/02_2025/7fg2_31574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fg2_31574/02_2025/7fg2_31574.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.58, per 1000 atoms: 0.60
  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: 2.60
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.07
  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: 3.08

  Time building geometry restraints manager: 3.00 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.170
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.690
-------------------------------------------------------------------------------
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   9553  Z= 0.451
  Angle     :  1.134   9.825  12992  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 : 32.64
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.021   0.003   TRP A1102 
 HIS   0.006   0.002   HIS A1083 
 PHE   0.028   0.003   PHE A 797 
 TYR   0.027   0.003   TYR A 789 
 ARG   0.011   0.001   ARG A 319 

*********************** 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  : 0.993 
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: 0.7359 (t)
REVERT: A  137 ASN cc_start: 0.6800 (p0) cc_final: 0.6326 (p0)
REVERT: A  220 PHE cc_start: 0.7007 (t80) cc_final: 0.6699 (t80)
REVERT: A  223 LEU cc_start: 0.8221 (mp) cc_final: 0.8004 (mp)
REVERT: A  350 VAL cc_start: 0.8770 (p) cc_final: 0.8000 (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: 0.7463 (m-10)
REVERT: A  738 CYS cc_start: 0.9078 (t) cc_final: 0.8693 (t)
REVERT: A  818 ILE cc_start: 0.7786 (mt) cc_final: 0.6824 (mt)
REVERT: A  823 PHE cc_start: 0.7910 (t80) cc_final: 0.7635 (t80)
REVERT: A  900 MET cc_start: 0.7036 (mpp) cc_final: 0.6520 (mpp)
REVERT: A 1010 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8271 (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: 0.4704 (pmm)
  outliers start: 2
  outliers final: 0
  residues processed: 222
  average time/residue: 0.2122
  time to fit residues: 65.9905
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  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    0.0770
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0070
   chunk 30 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 108 optimal weight:   20.0000
   overall best weight:    0.5356

-------------------------------------------------------------------------------
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 655 HIS
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

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.181954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152539 restraints weight = 26168.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.154713 restraints weight = 17617.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.156322 restraints weight = 13094.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6359
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9553  Z= 0.215
  Angle     :  0.765  10.967  12992  Z= 0.414
  Chirality :  0.049   0.240   1465
  Planarity :  0.006   0.065   1689
  Dihedral  :  7.302  66.218   1296
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 13.40 %
    Favored  : 86.18 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.02 %
    Favored  : 94.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.44 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.23), residues: 1194
  helix:  0.26 (0.35), residues: 220
  sheet: -1.75 (0.36), residues: 195
  loop : -3.34 (0.20), residues: 779

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.005   0.001   HIS A 655 
 PHE   0.022   0.002   PHE A 592 
 TYR   0.020   0.002   TYR A 451 
 ARG   0.006   0.001   ARG A 190 

*********************** 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
  252 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 247
  time to evaluate  : 0.963 
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   52 GLN cc_start: 0.8053 (pp30) cc_final: 0.7695 (pp30)
REVERT: A  137 ASN cc_start: 0.5651 (p0) cc_final: 0.5306 (p0)
REVERT: A  221 SER cc_start: 0.7578 (t) cc_final: 0.7354 (m)
REVERT: A  274 THR cc_start: 0.7996 (t) cc_final: 0.7626 (t)
REVERT: A  350 VAL cc_start: 0.8265 (p) cc_final: 0.7734 (p)
REVERT: A  400 PHE cc_start: 0.7926 (p90) cc_final: 0.7569 (p90)
REVERT: A  608 VAL cc_start: 0.5575 (p) cc_final: 0.5216 (p)
REVERT: A  729 VAL cc_start: 0.8290 (t) cc_final: 0.8044 (p)
REVERT: A  773 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6752 (tm-30)
REVERT: A  777 ASN cc_start: 0.8512 (m110) cc_final: 0.8197 (m110)
REVERT: A  900 MET cc_start: 0.6494 (mpp) cc_final: 0.6236 (mpp)
REVERT: A  933 LYS cc_start: 0.8845 (tttm) cc_final: 0.8330 (tttt)
REVERT: A 1005 GLN cc_start: 0.8604 (tp40) cc_final: 0.8364 (tp40)
REVERT: A 1010 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7914 (tp40)
REVERT: A 1027 THR cc_start: 0.8057 (m) cc_final: 0.7791 (m)
REVERT: A 1028 LYS cc_start: 0.6143 (tptt) cc_final: 0.5929 (tptt)
REVERT: A 1043 CYS cc_start: 0.3880 (m) cc_final: 0.3454 (m)
REVERT: A 1049 LEU cc_start: 0.6482 (mt) cc_final: 0.6078 (mp)
REVERT: A 1064 HIS cc_start: 0.6033 (m170) cc_final: 0.5595 (m170)
REVERT: D   33 TYR cc_start: 0.5875 (m-80) cc_final: 0.5578 (m-80)
  outliers start: 5
  outliers final: 0
  residues processed: 248
  average time/residue: 0.2115
  time to fit residues: 73.1737
Evaluate side-chains
  188 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 89 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 115 optimal weight:    9.9990
   chunk 103 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 50 optimal weight:    0.4980
   chunk 79 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 606 ASN
** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.179824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.149568 restraints weight = 26358.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.151964 restraints weight = 17131.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.153674 restraints weight = 12460.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6451
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9553  Z= 0.254
  Angle     :  0.759  10.819  12992  Z= 0.408
  Chirality :  0.048   0.179   1465
  Planarity :  0.005   0.062   1689
  Dihedral  :  7.086  64.517   1296
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 15.08 %
    Favored  : 84.51 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  5.41 %
    Favored  : 94.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.44 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.23), residues: 1194
  helix:  0.23 (0.34), residues: 228
  sheet: -1.96 (0.35), residues: 190
  loop : -3.24 (0.20), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 152 
 HIS   0.007   0.001   HIS A 655 
 PHE   0.024   0.002   PHE A1121 
 TYR   0.015   0.002   TYR A 451 
 ARG   0.005   0.001   ARG A 983 

*********************** 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
  217 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 215
  time to evaluate  : 1.007 
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   52 GLN cc_start: 0.8136 (pp30) cc_final: 0.7799 (pp30)
REVERT: A  221 SER cc_start: 0.7645 (t) cc_final: 0.7343 (m)
REVERT: A  274 THR cc_start: 0.7959 (t) cc_final: 0.7547 (t)
REVERT: A  350 VAL cc_start: 0.8360 (p) cc_final: 0.7260 (p)
REVERT: A  400 PHE cc_start: 0.7988 (p90) cc_final: 0.7499 (p90)
REVERT: A  732 THR cc_start: 0.8759 (p) cc_final: 0.8512 (p)
REVERT: A  738 CYS cc_start: 0.8485 (t) cc_final: 0.8279 (t)
REVERT: A  773 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6681 (tm-30)
REVERT: A  777 ASN cc_start: 0.8557 (m110) cc_final: 0.8120 (m110)
REVERT: A  900 MET cc_start: 0.7282 (mpp) cc_final: 0.6721 (mpp)
REVERT: A  985 ASP cc_start: 0.7792 (m-30) cc_final: 0.7515 (m-30)
REVERT: A 1005 GLN cc_start: 0.8712 (tp40) cc_final: 0.8502 (tp40)
REVERT: A 1010 GLN cc_start: 0.8459 (tp-100) cc_final: 0.7620 (tp-100)
REVERT: A 1012 LEU cc_start: 0.8864 (mt) cc_final: 0.8633 (mp)
REVERT: A 1031 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7285 (mt-10)
REVERT: A 1052 PHE cc_start: 0.8033 (m-10) cc_final: 0.7643 (m-10)
REVERT: D    5 LEU cc_start: 0.8358 (mt) cc_final: 0.7655 (mt)
REVERT: D   33 TYR cc_start: 0.6174 (m-80) cc_final: 0.5801 (m-80)
REVERT: D   85 ASN cc_start: 0.6448 (m-40) cc_final: 0.6014 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 215
  average time/residue: 0.2188
  time to fit residues: 65.6003
Evaluate side-chains
  171 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 87 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 606 ASN
** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 655 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.182423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.152353 restraints weight = 26402.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.154866 restraints weight = 16821.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.156636 restraints weight = 12055.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6384
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9553  Z= 0.196
  Angle     :  0.696   9.735  12992  Z= 0.375
  Chirality :  0.047   0.161   1465
  Planarity :  0.005   0.056   1689
  Dihedral  :  6.848  65.989   1296
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 13.15 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.57 %
    Favored  : 96.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.44 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.23), residues: 1194
  helix:  0.37 (0.34), residues: 231
  sheet: -1.67 (0.35), residues: 192
  loop : -3.12 (0.20), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  37 
 HIS   0.006   0.001   HIS A 655 
 PHE   0.022   0.002   PHE A 592 
 TYR   0.015   0.001   TYR D  98 
 ARG   0.003   0.000   ARG A1091 

*********************** 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
  221 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 218
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8101 (pp30) cc_final: 0.7657 (pp30)
REVERT: A   80 ASP cc_start: 0.8215 (p0) cc_final: 0.7969 (p0)
REVERT: A  153 MET cc_start: 0.2357 (mtt) cc_final: 0.1804 (mtp)
REVERT: A  350 VAL cc_start: 0.8339 (p) cc_final: 0.7212 (p)
REVERT: A  400 PHE cc_start: 0.7897 (p90) cc_final: 0.7529 (p90)
REVERT: A  563 GLN cc_start: 0.7302 (pt0) cc_final: 0.7073 (pt0)
REVERT: A  613 GLN cc_start: 0.7947 (mt0) cc_final: 0.7443 (pt0)
REVERT: A  640 SER cc_start: 0.7658 (p) cc_final: 0.7179 (t)
REVERT: A  646 ARG cc_start: 0.7360 (mtp85) cc_final: 0.7128 (tpt170)
REVERT: A  732 THR cc_start: 0.8698 (p) cc_final: 0.8383 (p)
REVERT: A  773 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6561 (tm-30)
REVERT: A  774 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8078 (mm-40)
REVERT: A  777 ASN cc_start: 0.8494 (m110) cc_final: 0.8049 (m110)
REVERT: A  858 LEU cc_start: 0.8562 (mt) cc_final: 0.8190 (mt)
REVERT: A  859 THR cc_start: 0.8471 (t) cc_final: 0.8138 (m)
REVERT: A  900 MET cc_start: 0.7079 (mpp) cc_final: 0.6642 (mpp)
REVERT: A  985 ASP cc_start: 0.7792 (m-30) cc_final: 0.7473 (m-30)
REVERT: A 1002 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7220 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8730 (tp40) cc_final: 0.8426 (tp40)
REVERT: A 1010 GLN cc_start: 0.8359 (tp-100) cc_final: 0.7844 (tp40)
REVERT: A 1031 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7259 (mt-10)
REVERT: A 1064 HIS cc_start: 0.6610 (m170) cc_final: 0.6397 (m170)
REVERT: D   33 TYR cc_start: 0.6173 (m-80) cc_final: 0.5920 (m-80)
REVERT: D   85 ASN cc_start: 0.6453 (m-40) cc_final: 0.5968 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 219
  average time/residue: 0.2112
  time to fit residues: 65.1200
Evaluate side-chains
  174 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0470
   chunk 30 optimal weight:    0.0970
   chunk 57 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 58 optimal weight:    0.4980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
A 606 ASN
A 655 HIS
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.184473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.154462 restraints weight = 26310.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.156837 restraints weight = 16664.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.158666 restraints weight = 12092.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6337
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9553  Z= 0.178
  Angle     :  0.672   9.173  12992  Z= 0.361
  Chirality :  0.046   0.163   1465
  Planarity :  0.005   0.051   1689
  Dihedral  :  6.471  64.647   1296
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.73 %
    Favored  : 86.93 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.28 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.23), residues: 1194
  helix:  0.81 (0.36), residues: 216
  sheet: -1.48 (0.35), residues: 206
  loop : -3.04 (0.21), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.008   0.001   HIS A 655 
 PHE   0.025   0.001   PHE A1075 
 TYR   0.019   0.001   TYR A1110 
 ARG   0.004   0.000   ARG A 905 

*********************** 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
  221 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 219
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7778 (pp30) cc_final: 0.7280 (pp30)
REVERT: A   80 ASP cc_start: 0.8226 (p0) cc_final: 0.7980 (p0)
REVERT: A  153 MET cc_start: 0.2308 (mtt) cc_final: 0.1913 (mtp)
REVERT: A  182 LYS cc_start: 0.6222 (mtmm) cc_final: 0.5680 (mmmt)
REVERT: A  220 PHE cc_start: 0.7032 (t80) cc_final: 0.6720 (t80)
REVERT: A  350 VAL cc_start: 0.8411 (p) cc_final: 0.7244 (p)
REVERT: A  400 PHE cc_start: 0.7827 (p90) cc_final: 0.7398 (p90)
REVERT: A  613 GLN cc_start: 0.7784 (mt0) cc_final: 0.7187 (pt0)
REVERT: A  640 SER cc_start: 0.7590 (p) cc_final: 0.7130 (t)
REVERT: A  732 THR cc_start: 0.8710 (p) cc_final: 0.8313 (p)
REVERT: A  747 THR cc_start: 0.7315 (m) cc_final: 0.6985 (p)
REVERT: A  773 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6373 (tm-30)
REVERT: A  774 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7832 (mm110)
REVERT: A  777 ASN cc_start: 0.8425 (m110) cc_final: 0.7999 (m110)
REVERT: A  786 LYS cc_start: 0.5365 (ptpt) cc_final: 0.4869 (pptt)
REVERT: A  935 GLN cc_start: 0.7720 (tp-100) cc_final: 0.6797 (tp-100)
REVERT: A  985 ASP cc_start: 0.7665 (m-30) cc_final: 0.7385 (m-30)
REVERT: A 1002 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7294 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8672 (tp40) cc_final: 0.8407 (tp40)
REVERT: A 1010 GLN cc_start: 0.8435 (tp-100) cc_final: 0.7878 (tp40)
REVERT: A 1028 LYS cc_start: 0.6715 (tptp) cc_final: 0.6037 (ttpt)
REVERT: A 1049 LEU cc_start: 0.6920 (mt) cc_final: 0.6626 (mp)
REVERT: A 1075 PHE cc_start: 0.6539 (m-10) cc_final: 0.6123 (m-10)
REVERT: D   33 TYR cc_start: 0.5728 (m-80) cc_final: 0.5492 (m-80)
REVERT: D   35 MET cc_start: -0.0052 (ptt) cc_final: -0.0759 (ptt)
REVERT: D   37 TRP cc_start: 0.1343 (m-90) cc_final: 0.0760 (m-90)
REVERT: D   85 ASN cc_start: 0.6382 (m-40) cc_final: 0.5747 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 219
  average time/residue: 0.2152
  time to fit residues: 66.0790
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  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 31 optimal weight:   20.0000
   chunk 79 optimal weight:    0.0170
   chunk 19 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 106 optimal weight:   30.0000
   chunk 18 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    2.1624

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

Flipped N/Q/H residues before XYZ refinement:
A 606 ASN
A 655 HIS
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.180594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.149881 restraints weight = 26706.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152336 restraints weight = 17052.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.154078 restraints weight = 12360.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6431
moved from start:          0.3967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9553  Z= 0.249
  Angle     :  0.718   8.863  12992  Z= 0.384
  Chirality :  0.047   0.170   1465
  Planarity :  0.005   0.053   1689
  Dihedral  :  6.642  65.352   1296
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 13.57 %
    Favored  : 86.10 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.61 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.23), residues: 1194
  helix:  0.43 (0.34), residues: 230
  sheet: -1.74 (0.36), residues: 188
  loop : -3.04 (0.20), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 633 
 HIS   0.009   0.001   HIS A 655 
 PHE   0.021   0.002   PHE A1075 
 TYR   0.023   0.002   TYR A1110 
 ARG   0.006   0.001   ARG A 685 

*********************** 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
  207 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 205
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.8287 (p0) cc_final: 0.8024 (p0)
REVERT: A  153 MET cc_start: 0.2510 (mtt) cc_final: 0.1870 (mtp)
REVERT: A  220 PHE cc_start: 0.7682 (t80) cc_final: 0.7457 (t80)
REVERT: A  350 VAL cc_start: 0.8509 (p) cc_final: 0.7465 (p)
REVERT: A  400 PHE cc_start: 0.7863 (p90) cc_final: 0.7461 (p90)
REVERT: A  613 GLN cc_start: 0.8150 (mt0) cc_final: 0.7510 (pt0)
REVERT: A  640 SER cc_start: 0.7490 (p) cc_final: 0.6962 (t)
REVERT: A  732 THR cc_start: 0.8599 (p) cc_final: 0.8391 (p)
REVERT: A  747 THR cc_start: 0.7508 (m) cc_final: 0.7063 (p)
REVERT: A  773 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6480 (tm-30)
REVERT: A  777 ASN cc_start: 0.8447 (m110) cc_final: 0.8112 (m110)
REVERT: A  900 MET cc_start: 0.6772 (mpp) cc_final: 0.6544 (mpp)
REVERT: A  985 ASP cc_start: 0.7716 (m-30) cc_final: 0.7442 (m-30)
REVERT: A 1002 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7213 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8742 (tp40) cc_final: 0.8394 (tp-100)
REVERT: A 1010 GLN cc_start: 0.8347 (tp-100) cc_final: 0.8020 (tp-100)
REVERT: A 1058 HIS cc_start: 0.7224 (m90) cc_final: 0.6912 (m90)
REVERT: D   33 TYR cc_start: 0.6019 (m-80) cc_final: 0.5732 (m-80)
REVERT: D   85 ASN cc_start: 0.7211 (m-40) cc_final: 0.5768 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 205
  average time/residue: 0.2126
  time to fit residues: 62.4799
Evaluate side-chains
  163 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 105 optimal weight:    0.4980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 606 ASN
A 655 HIS
A 710 ASN
A 926 GLN
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.182703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.152795 restraints weight = 26765.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.155210 restraints weight = 17022.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.157089 restraints weight = 12310.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6373
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9553  Z= 0.199
  Angle     :  0.687   8.698  12992  Z= 0.368
  Chirality :  0.046   0.167   1465
  Planarity :  0.005   0.043   1689
  Dihedral  :  6.463  64.101   1296
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.40 %
    Favored  : 87.27 %
  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 : 1.92 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.23), residues: 1194
  helix:  0.74 (0.36), residues: 217
  sheet: -1.35 (0.35), residues: 215
  loop : -3.08 (0.20), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 633 
 HIS   0.009   0.001   HIS A 655 
 PHE   0.033   0.002   PHE A1121 
 TYR   0.017   0.001   TYR D  98 
 ARG   0.005   0.001   ARG A 190 

*********************** 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
  208 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.960 
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: 0.7920 (pp30) cc_final: 0.7535 (pp30)
REVERT: A   80 ASP cc_start: 0.8153 (p0) cc_final: 0.7904 (p0)
REVERT: A  153 MET cc_start: 0.2626 (mtt) cc_final: 0.2093 (mtp)
REVERT: A  350 VAL cc_start: 0.8471 (p) cc_final: 0.7349 (p)
REVERT: A  400 PHE cc_start: 0.7724 (p90) cc_final: 0.7337 (p90)
REVERT: A  613 GLN cc_start: 0.8007 (mt0) cc_final: 0.7398 (pt0)
REVERT: A  640 SER cc_start: 0.7551 (p) cc_final: 0.7056 (t)
REVERT: A  747 THR cc_start: 0.7354 (m) cc_final: 0.7020 (p)
REVERT: A  773 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6496 (tm-30)
REVERT: A  774 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8015 (mm110)
REVERT: A  777 ASN cc_start: 0.8424 (m110) cc_final: 0.8130 (m110)
REVERT: A  786 LYS cc_start: 0.5629 (ptpt) cc_final: 0.4919 (pptt)
REVERT: A  935 GLN cc_start: 0.7540 (tp-100) cc_final: 0.7313 (tp40)
REVERT: A  985 ASP cc_start: 0.7682 (m-30) cc_final: 0.7376 (m-30)
REVERT: A 1002 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8737 (tp40) cc_final: 0.8488 (tp40)
REVERT: A 1010 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7943 (tp40)
REVERT: A 1014 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.8152 (ttm170)
REVERT: A 1075 PHE cc_start: 0.5956 (m-10) cc_final: 0.5615 (m-10)
REVERT: D   85 ASN cc_start: 0.7183 (m-40) cc_final: 0.5676 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2208
  time to fit residues: 64.8867
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  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 106 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0980
   chunk 96 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 95 optimal weight:    0.6980
   chunk 76 optimal weight:    0.1980
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 ASN
A 655 HIS
** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.185197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.154870 restraints weight = 26876.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.157560 restraints weight = 16878.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.159438 restraints weight = 11907.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6308
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9553  Z= 0.178
  Angle     :  0.681   9.690  12992  Z= 0.363
  Chirality :  0.046   0.171   1465
  Planarity :  0.005   0.067   1689
  Dihedral  :  6.373  62.152   1296
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.81 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.35 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.23), residues: 1194
  helix:  0.73 (0.36), residues: 218
  sheet: -1.41 (0.35), residues: 219
  loop : -2.95 (0.20), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  37 
 HIS   0.007   0.001   HIS A 655 
 PHE   0.038   0.001   PHE A 220 
 TYR   0.014   0.001   TYR D  98 
 ARG   0.014   0.001   ARG A 577 

*********************** 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
  213 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 1.036 
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: symmetry clash
REVERT: A   52 GLN cc_start: 0.7902 (pp30) cc_final: 0.7572 (pp30)
REVERT: A   80 ASP cc_start: 0.8144 (p0) cc_final: 0.7921 (p0)
REVERT: A  153 MET cc_start: 0.2651 (mtt) cc_final: 0.2192 (mtp)
REVERT: A  350 VAL cc_start: 0.8359 (p) cc_final: 0.7189 (p)
REVERT: A  374 PHE cc_start: 0.5588 (p90) cc_final: 0.4852 (p90)
REVERT: A  400 PHE cc_start: 0.7673 (p90) cc_final: 0.7396 (p90)
REVERT: A  640 SER cc_start: 0.7425 (p) cc_final: 0.7013 (t)
REVERT: A  727 LEU cc_start: 0.8232 (mt) cc_final: 0.7833 (mt)
REVERT: A  731 MET cc_start: 0.8100 (mtt) cc_final: 0.7879 (mtm)
REVERT: A  732 THR cc_start: 0.8582 (p) cc_final: 0.8269 (p)
REVERT: A  747 THR cc_start: 0.7150 (m) cc_final: 0.6817 (p)
REVERT: A  773 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6704 (tm-30)
REVERT: A  774 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7990 (mm110)
REVERT: A  777 ASN cc_start: 0.8354 (m110) cc_final: 0.8131 (m110)
REVERT: A  786 LYS cc_start: 0.5279 (ptpt) cc_final: 0.4506 (pptt)
REVERT: A  985 ASP cc_start: 0.7662 (m-30) cc_final: 0.7311 (m-30)
REVERT: A 1002 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7298 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8720 (tp40) cc_final: 0.8368 (tp40)
REVERT: A 1010 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8106 (tp40)
REVERT: A 1049 LEU cc_start: 0.6886 (mt) cc_final: 0.6634 (mp)
REVERT: A 1075 PHE cc_start: 0.6032 (m-10) cc_final: 0.5365 (m-10)
REVERT: A 1076 THR cc_start: 0.7843 (m) cc_final: 0.7595 (p)
REVERT: D   33 TYR cc_start: 0.4632 (m-80) cc_final: 0.4422 (m-80)
REVERT: D   85 ASN cc_start: 0.7608 (m-40) cc_final: 0.5676 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2245
  time to fit residues: 66.2069
Evaluate side-chains
  179 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 54 optimal weight:    0.3980
   chunk 20 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0470
   chunk 3 optimal weight:    0.0980
   chunk 24 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 655 HIS
** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 GLN
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.186757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.156875 restraints weight = 26523.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.159489 restraints weight = 16902.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.161316 restraints weight = 12051.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6268
moved from start:          0.5099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9553  Z= 0.173
  Angle     :  0.673   9.967  12992  Z= 0.359
  Chirality :  0.046   0.272   1465
  Planarity :  0.005   0.045   1689
  Dihedral  :  6.131  58.333   1296
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 11.73 %
    Favored  : 87.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.23), residues: 1194
  helix:  0.66 (0.36), residues: 217
  sheet: -1.10 (0.36), residues: 210
  loop : -2.92 (0.20), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 107 
 HIS   0.006   0.001   HIS A 655 
 PHE   0.029   0.001   PHE A 220 
 TYR   0.014   0.001   TYR A 453 
 ARG   0.008   0.001   ARG A 357 

*********************** 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
  212 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.281 
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: 0.7938 (pp30) cc_final: 0.7661 (pp30)
REVERT: A  118 LEU cc_start: 0.7580 (tp) cc_final: 0.7366 (tp)
REVERT: A  153 MET cc_start: 0.2877 (mtt) cc_final: 0.2444 (mtt)
REVERT: A  220 PHE cc_start: 0.7512 (t80) cc_final: 0.7079 (t80)
REVERT: A  291 CYS cc_start: 0.7494 (p) cc_final: 0.7149 (p)
REVERT: A  350 VAL cc_start: 0.8300 (p) cc_final: 0.7028 (p)
REVERT: A  374 PHE cc_start: 0.5400 (p90) cc_final: 0.4680 (p90)
REVERT: A  400 PHE cc_start: 0.7565 (p90) cc_final: 0.7063 (p90)
REVERT: A  731 MET cc_start: 0.8327 (mtt) cc_final: 0.7886 (mtm)
REVERT: A  732 THR cc_start: 0.8524 (p) cc_final: 0.8037 (p)
REVERT: A  747 THR cc_start: 0.7152 (m) cc_final: 0.6841 (p)
REVERT: A  773 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6435 (tm-30)
REVERT: A  777 ASN cc_start: 0.8393 (m110) cc_final: 0.8076 (m110)
REVERT: A  786 LYS cc_start: 0.5107 (ptpt) cc_final: 0.4585 (pptt)
REVERT: A 1002 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8671 (tp40) cc_final: 0.8318 (tp40)
REVERT: A 1043 CYS cc_start: 0.3872 (m) cc_final: 0.2622 (m)
REVERT: A 1049 LEU cc_start: 0.6701 (mt) cc_final: 0.5847 (mp)
REVERT: A 1075 PHE cc_start: 0.6007 (m-10) cc_final: 0.5229 (m-10)
REVERT: A 1076 THR cc_start: 0.7776 (m) cc_final: 0.7530 (p)
REVERT: D   85 ASN cc_start: 0.7345 (m-40) cc_final: 0.5359 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2234
  time to fit residues: 66.6897
Evaluate side-chains
  180 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0000
   chunk 8 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 115 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 655 HIS
A1054 GLN
A1058 HIS
A1088 HIS
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.184997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.155113 restraints weight = 26846.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.157808 restraints weight = 16840.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.159663 restraints weight = 11844.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6304
moved from start:          0.5214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9553  Z= 0.192
  Angle     :  0.683   9.674  12992  Z= 0.363
  Chirality :  0.047   0.226   1465
  Planarity :  0.005   0.043   1689
  Dihedral  :  6.106  58.894   1296
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.56 %
    Favored  : 87.10 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.87 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.23), residues: 1194
  helix:  0.76 (0.36), residues: 217
  sheet: -1.26 (0.35), residues: 215
  loop : -2.86 (0.20), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP D 107 
 HIS   0.007   0.001   HIS A 655 
 PHE   0.039   0.002   PHE A  55 
 TYR   0.013   0.001   TYR A 453 
 ARG   0.007   0.001   ARG A 577 

********************** REFINEMENT MACRO_CYCLE 10 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
  202 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 200
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7176 (m-30) cc_final: 0.6933 (m-30)
REVERT: A   55 PHE cc_start: 0.6525 (m-10) cc_final: 0.6214 (m-10)
REVERT: A  153 MET cc_start: 0.2895 (mtt) cc_final: 0.2446 (mtt)
REVERT: A  220 PHE cc_start: 0.7611 (t80) cc_final: 0.7197 (t80)
REVERT: A  350 VAL cc_start: 0.8331 (p) cc_final: 0.7118 (p)
REVERT: A  374 PHE cc_start: 0.5535 (p90) cc_final: 0.4980 (p90)
REVERT: A  400 PHE cc_start: 0.7585 (p90) cc_final: 0.7352 (p90)
REVERT: A  725 GLU cc_start: 0.7086 (tt0) cc_final: 0.6874 (tt0)
REVERT: A  727 LEU cc_start: 0.8015 (mt) cc_final: 0.7639 (mt)
REVERT: A  731 MET cc_start: 0.8371 (mtt) cc_final: 0.8034 (mtm)
REVERT: A  747 THR cc_start: 0.6975 (m) cc_final: 0.6664 (p)
REVERT: A  773 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6279 (tm-30)
REVERT: A  777 ASN cc_start: 0.8346 (m110) cc_final: 0.8002 (m110)
REVERT: A  786 LYS cc_start: 0.5273 (ptpt) cc_final: 0.4492 (pptt)
REVERT: A  985 ASP cc_start: 0.7716 (m-30) cc_final: 0.7451 (m-30)
REVERT: A  986 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7886 (mmtm)
REVERT: A 1002 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7419 (tm-30)
REVERT: A 1005 GLN cc_start: 0.8676 (tp40) cc_final: 0.8347 (tp40)
REVERT: A 1010 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8062 (tp40)
REVERT: A 1075 PHE cc_start: 0.5923 (m-10) cc_final: 0.5013 (m-10)
REVERT: A 1076 THR cc_start: 0.7797 (m) cc_final: 0.7567 (p)
REVERT: D   85 ASN cc_start: 0.7387 (m-40) cc_final: 0.5320 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 201
  average time/residue: 0.2234
  time to fit residues: 62.3453
Evaluate side-chains
  171 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 11 optimal weight:    9.9990
   chunk 108 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 76 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 117 optimal weight:    3.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 655 HIS
** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4381 r_free = 0.4381 target = 0.185142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.155143 restraints weight = 26772.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.157840 restraints weight = 16828.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.159728 restraints weight = 11819.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6304
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9553  Z= 0.191
  Angle     :  0.686   9.836  12992  Z= 0.365
  Chirality :  0.047   0.352   1465
  Planarity :  0.004   0.043   1689
  Dihedral  :  6.061  57.044   1296
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.23 %
    Favored  : 87.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.23), residues: 1194
  helix:  0.64 (0.36), residues: 214
  sheet: -1.21 (0.36), residues: 209
  loop : -2.83 (0.20), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D 107 
 HIS   0.007   0.001   HIS A 655 
 PHE   0.035   0.002   PHE A  55 
 TYR   0.013   0.001   TYR A 453 
 ARG   0.007   0.001   ARG A 577 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3146.30 seconds
wall clock time: 57 minutes 17.64 seconds (3437.64 seconds total)