Starting phenix.real_space_refine
on Wed Mar 12 07:43:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9coo_45787/03_2025/9coo_45787.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9coo_45787/03_2025/9coo_45787.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9coo_45787/03_2025/9coo_45787.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9coo_45787/03_2025/9coo_45787.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9coo_45787/03_2025/9coo_45787.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9coo_45787/03_2025/9coo_45787.cif"
  }
  resolution = 3.73
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     S      36      5.16       5
     C    4685      2.51       5
     N    1266      2.21       5
     O    1503      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7493
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3170
          Classifications: {'peptide': 423}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 11, 'TRANS': 411}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 162
          Unresolved non-hydrogen angles: 196
          Unresolved non-hydrogen dihedrals: 155
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 101
    Chain: "B"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 926
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 6, 'TRANS': 121}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 54
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "H"
      Number of atoms: 923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 923
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 6, 'TRANS': 118}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "L"
      Number of atoms: 769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 769
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 57
          Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "N"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 859
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 67
    Chain: "R"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 801
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 7, 'TRANS': 112}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 94
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 91
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "R"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.46, per 1000 atoms: 0.73
  Number of scatterers: 7493
  At special positions: 0
  Unit cell: (104.58, 117.86, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      3     19.99
     S      36     16.00
     O    1503      8.00
     N    1266      7.00
     C    4685      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  68 " - pdb=" SG  CYS R  82 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  75 " - pdb=" SG  CYS R  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  89 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 109 " - pdb=" SG  CYS R 121 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 116 " - pdb=" SG  CYS R 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 128 " - pdb=" SG  CYS R 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 148 " - pdb=" SG  CYS R 160 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 155 " - pdb=" SG  CYS R 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 167 " - pdb=" SG  CYS R 184 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A4601 " - " ASN A3336 "
      " NAG A4602 " - " ASN A3101 "
  Time building additional restraints: 1.92
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 11 sheets defined
      13.0% alpha, 30.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'B' and resid 335 through 353
      removed outlier: 4.163A  pdb=" N   ALA B 339 " --> pdb=" O   PRO B 335 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TYR B 342 " --> pdb=" O   SER B 338 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   ILE B 349 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 370
      removed outlier: 3.783A  pdb=" N   ALA B 365 " --> pdb=" O   ALA B 361 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET B 370 " --> pdb=" O   GLN B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 388
    Processing helix  chain 'B' and resid 391 through 406
      removed outlier: 3.612A  pdb=" N   GLU B 398 " --> pdb=" O   GLU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 428
      removed outlier: 4.077A  pdb=" N   SER B 422 " --> pdb=" O   GLY B 418 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LEU B 428 " --> pdb=" O   PHE B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 448
    Processing helix  chain 'B' and resid 451 through 469
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.937A  pdb=" N   LEU L  89 " --> pdb=" O   PRO L  86 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.756A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 88
      No H-bonds generated for 'chain 'R' and resid 86 through 88'
    Processing helix  chain 'R' and resid 137 through 142
      removed outlier: 3.855A  pdb=" N   SER R 142 " --> pdb=" O   SER R 138 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 184 through 189
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2825 through 2831
      removed outlier: 3.570A  pdb=" N   VAL A2828 " --> pdb=" O   HIS A2839 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   HIS A2839 " --> pdb=" O   VAL A2828 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   PHE A2846 " --> pdb=" O   ALA A2849 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA A2849 " --> pdb=" O   PHE A2846 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A2858 " --> pdb=" O   LEU A2869 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   THR A2866 " --> pdb=" O   LYS A2892 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLU A2868 " --> pdb=" O   PHE A2890 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   PHE A2890 " --> pdb=" O   GLU A2868 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A2906 " --> pdb=" O   TYR A2889 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ILE A2895 " --> pdb=" O   PHE A2900 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 2918 through 2922
    current: chain 'A' and resid 2939 through 2951
      removed outlier: 3.649A  pdb=" N   ASN A2961 " --> pdb=" O   GLN A2972 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 2968 through 2975
    current: chain 'A' and resid 3000 through 3009
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 3015 through 3023
    current: chain 'A' and resid 3030 through 3031
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 3030 through 3031
    current: chain 'A' and resid 3064 through 3074
      removed outlier: 4.172A  pdb=" N   ASP A3069 " --> pdb=" O   ARG A3092 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG A3092 " --> pdb=" O   ASP A3069 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER A3090 " --> pdb=" O   LEU A3071 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR A3098 " --> pdb=" O   ALA A3091 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR A3096 " --> pdb=" O   PHE A3093 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 3337 through 3344
      removed outlier: 3.669A  pdb=" N   ALA A3364 " --> pdb=" O   THR A3385 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR A3385 " --> pdb=" O   ALA A3364 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A3366 " --> pdb=" O   GLY A3383 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLY A3383 " --> pdb=" O   LEU A3366 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'H' and resid 46 through 51
      removed outlier: 4.836A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY H  33 " --> pdb=" O   ARG H  99 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA6, first strand: chain 'L' and resid 39 through 44
      removed outlier: 6.306A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'L' and resid 59 through 60
    current: chain 'L' and resid 102 through 103
    Processing sheet with id=AA7, first strand: chain 'N' and resid 6 through 7
      removed outlier: 3.549A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 13
      removed outlier: 6.434A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 120 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   SER N 122 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL N  12 " --> pdb=" O   SER N 122 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   MET N  34 " --> pdb=" O   ILE N  51 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 72 through 74
    Processing sheet with id=AB1, first strand: chain 'R' and resid 113 through 115
    Processing sheet with id=AB2, first strand: chain 'R' and resid 152 through 154
      removed outlier: 3.590A  pdb=" N   ILE R 161 " --> pdb=" O   PHE R 153 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    759 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: 2.36

  Time building geometry restraints manager: 2.31 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: 2471
        1.34 -     1.46: 1309
        1.46 -     1.57: 3811
        1.57 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 7638
  Sorted by residual:
  bond pdb=" CB  ASP L  66 "
       pdb=" CG  ASP L  66 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.30e+00
  bond pdb=" CB  ASN B 379 "
       pdb=" CG  ASN B 379 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  bond pdb=" CB  GLU A2826 "
       pdb=" CG  GLU A2826 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.73e-01
  bond pdb=" CB  CYS H  96 "
       pdb=" SG  CYS H  96 "
    ideal  model  delta    sigma   weight residual
    1.808  1.775  0.033 3.30e-02 9.18e+02 9.73e-01
  bond pdb=" CA  ASN H  77 "
       pdb=" CB  ASN H  77 "
    ideal  model  delta    sigma   weight residual
    1.527  1.543 -0.015 1.61e-02 3.86e+03 9.17e-01
  ... (remaining 7633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 10183
        1.92 -     3.84: 185
        3.84 -     5.75: 25
        5.75 -     7.67: 11
        7.67 -     9.59: 4
  Bond angle restraints: 10408
  Sorted by residual:
  angle pdb=" CA  ARG B 345 "
        pdb=" CB  ARG B 345 "
        pdb=" CG  ARG B 345 "
      ideal   model   delta    sigma   weight residual
     114.10  121.08   -6.98 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" C2  NAG A4602 "
        pdb=" N2  NAG A4602 "
        pdb=" C7  NAG A4602 "
      ideal   model   delta    sigma   weight residual
     124.56  133.57   -9.01 3.00e+00 1.11e-01 9.03e+00
  angle pdb=" CB  ARG B 345 "
        pdb=" CG  ARG B 345 "
        pdb=" CD  ARG B 345 "
      ideal   model   delta    sigma   weight residual
     111.30  118.00   -6.70 2.30e+00 1.89e-01 8.49e+00
  angle pdb=" CA  LEU A2869 "
        pdb=" CB  LEU A2869 "
        pdb=" CG  LEU A2869 "
      ideal   model   delta    sigma   weight residual
     116.30  125.89   -9.59 3.50e+00 8.16e-02 7.51e+00
  angle pdb=" CB  MET A3007 "
        pdb=" CG  MET A3007 "
        pdb=" SD  MET A3007 "
      ideal   model   delta    sigma   weight residual
     112.70  120.87   -8.17 3.00e+00 1.11e-01 7.41e+00
  ... (remaining 10403 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.47: 3870
       16.47 -    32.93: 485
       32.93 -    49.40: 145
       49.40 -    65.87: 41
       65.87 -    82.34: 5
  Dihedral angle restraints: 4546
    sinusoidal: 1606
      harmonic: 2940
  Sorted by residual:
  dihedral pdb=" CB  CYS R 155 "
           pdb=" SG  CYS R 155 "
           pdb=" SG  CYS R 173 "
           pdb=" CB  CYS R 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.19   57.19     1      1.00e+01 1.00e-02 4.40e+01
  dihedral pdb=" CB  CYS R 109 "
           pdb=" SG  CYS R 109 "
           pdb=" SG  CYS R 121 "
           pdb=" CB  CYS R 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.47   56.47     1      1.00e+01 1.00e-02 4.30e+01
  dihedral pdb=" CB  CYS R  68 "
           pdb=" SG  CYS R  68 "
           pdb=" SG  CYS R  82 "
           pdb=" CB  CYS R  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.80  -53.80     1      1.00e+01 1.00e-02 3.93e+01
  ... (remaining 4543 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1017
       0.056 -    0.112: 160
       0.112 -    0.168: 25
       0.168 -    0.224: 0
       0.224 -    0.279: 2
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" C1  NAG A4602 "
            pdb=" ND2 ASN A3101 "
            pdb=" C2  NAG A4602 "
            pdb=" O5  NAG A4602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CG  LEU B 462 "
            pdb=" CB  LEU B 462 "
            pdb=" CD1 LEU B 462 "
            pdb=" CD2 LEU B 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" C2  NAG A4602 "
            pdb=" C1  NAG A4602 "
            pdb=" C3  NAG A4602 "
            pdb=" N2  NAG A4602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.33   -0.17 2.00e-01 2.50e+01 6.90e-01
  ... (remaining 1201 not shown)

  Planarity restraints: 1359
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A2971 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   ASN A2971 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ASN A2971 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLN A2972 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R  83 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO R  84 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO R  84 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R  84 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A2895 "    0.024 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO A2896 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A2896 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A2896 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1356 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 577
        2.73 -     3.27: 8002
        3.27 -     3.81: 12364
        3.81 -     4.36: 14118
        4.36 -     4.90: 24213
  Nonbonded interactions: 59274
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 448 "
            pdb=" ND2 ASN B 454 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" OD1 ASP R 170 "
            pdb="CA    CA R 903 "
     model   vdw
     2.226 2.510
  nonbonded pdb=" OE2 GLU R 101 "
            pdb="CA    CA R 901 "
     model   vdw
     2.233 2.510
  nonbonded pdb=" O   SER R 130 "
            pdb=" OG  SER R 130 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   TYR A3379 "
            pdb=" NZ  LYS A3380 "
     model   vdw
     2.236 3.120
  ... (remaining 59269 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:             3.040
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.270
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7638  Z= 0.226
  Angle     :  0.663   9.589  10408  Z= 0.334
  Chirality :  0.043   0.279   1204
  Planarity :  0.004   0.051   1357
  Dihedral  : 16.582  82.337   2620
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 32.36 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.26), residues: 1006
  helix: -0.50 (0.46), residues: 123
  sheet: -1.96 (0.24), residues: 441
  loop : -1.69 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  87 
 HIS   0.011   0.001   HIS N 104 
 PHE   0.015   0.001   PHE A3038 
 TYR   0.016   0.001   TYR B 342 
 ARG   0.003   0.000   ARG A2836 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7825 (tmm) cc_final: 0.6856 (tmm)
REVERT: A 3174 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7628 (mtpt)
REVERT: A 3340 ASP cc_start: 0.7895 (p0) cc_final: 0.7523 (m-30)
REVERT: B  456 LEU cc_start: 0.8882 (tp) cc_final: 0.8604 (tt)
REVERT: H   29 PHE cc_start: 0.8251 (t80) cc_final: 0.7677 (t80)
REVERT: H  108 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7257 (m-80)
REVERT: L   79 LEU cc_start: 0.7855 (tp) cc_final: 0.7254 (pp)
  outliers start: 11
  outliers final: 7
  residues processed: 109
  average time/residue: 0.1718
  time to fit residues: 26.2143
Evaluate side-chains
  106 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   84 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    0.2980
   chunk 25 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0970
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.112878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.099189 restraints weight = 22933.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.100833 restraints weight = 13710.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.101872 restraints weight = 9709.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.0837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7638  Z= 0.269
  Angle     :  0.645   9.661  10408  Z= 0.329
  Chirality :  0.044   0.328   1204
  Planarity :  0.004   0.048   1357
  Dihedral  :  5.752  53.560   1146
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 28.93 %
    Favored  : 66.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.41 (0.26), residues: 1006
  helix:  0.38 (0.49), residues: 121
  sheet: -1.91 (0.25), residues: 425
  loop : -1.69 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP R 165 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.017   0.002   PHE B 424 
 TYR   0.016   0.002   TYR A3177 
 ARG   0.003   0.001   ARG H  99 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A 2843 MET cc_start: 0.7759 (tmm) cc_final: 0.7044 (tmm)
REVERT: A 2933 CYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6081 (m)
REVERT: A 3106 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.7802 (m-40)
REVERT: A 3126 LEU cc_start: 0.7730 (tp) cc_final: 0.7496 (tp)
REVERT: A 3174 LYS cc_start: 0.7705 (mmtm) cc_final: 0.7442 (mtpt)
REVERT: B  456 LEU cc_start: 0.8623 (tp) cc_final: 0.8221 (tt)
REVERT: H  108 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6957 (m-80)
REVERT: R  168 ASP cc_start: 0.7877 (m-30) cc_final: 0.7153 (p0)
  outliers start: 32
  outliers final: 16
  residues processed: 124
  average time/residue: 0.1642
  time to fit residues: 28.7921
Evaluate side-chains
  110 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3021 HIS
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 85 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A2865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.111360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.097906 restraints weight = 23531.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.099397 restraints weight = 14614.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.100418 restraints weight = 10470.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   7638  Z= 0.325
  Angle     :  0.669   9.530  10408  Z= 0.341
  Chirality :  0.044   0.315   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  6.012  54.487   1146
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 26.68 %
    Favored  : 66.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.27), residues: 1006
  helix:  0.50 (0.50), residues: 121
  sheet: -2.00 (0.25), residues: 434
  loop : -1.68 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 165 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.015   0.002   PHE B 424 
 TYR   0.016   0.002   TYR A3177 
 ARG   0.004   0.001   ARG B 345 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 97
  time to evaluate  : 0.868 
Fit side-chains
REVERT: A 2843 MET cc_start: 0.7979 (tmm) cc_final: 0.7205 (tmm)
REVERT: A 2933 CYS cc_start: 0.6513 (OUTLIER) cc_final: 0.5988 (m)
REVERT: A 3126 LEU cc_start: 0.7869 (tp) cc_final: 0.7665 (tp)
REVERT: A 3166 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8290 (tptp)
REVERT: A 3359 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.4564 (pm20)
REVERT: B  360 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6523 (tt0)
REVERT: B  403 ASN cc_start: 0.8381 (t0) cc_final: 0.8131 (t0)
REVERT: B  426 GLU cc_start: 0.6874 (pp20) cc_final: 0.6617 (pp20)
REVERT: B  456 LEU cc_start: 0.8621 (tp) cc_final: 0.8406 (mt)
REVERT: B  463 ASN cc_start: 0.8010 (m-40) cc_final: 0.7799 (m110)
REVERT: B  464 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7715 (mp0)
REVERT: H  108 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6917 (m-80)
REVERT: N   45 ARG cc_start: 0.7537 (ttp-110) cc_final: 0.7227 (ttp-110)
REVERT: R  168 ASP cc_start: 0.7662 (m-30) cc_final: 0.7153 (p0)
  outliers start: 51
  outliers final: 31
  residues processed: 139
  average time/residue: 0.1795
  time to fit residues: 34.5626
Evaluate side-chains
  128 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 91
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3021 HIS
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3353 ASN
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3359 GLN
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain L residue   97 TYR
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 58 optimal weight:    0.2980
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A2839 HIS
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 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 = 0.4070 r_free = 0.4070 target = 0.112456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.098834 restraints weight = 23209.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.100489 restraints weight = 13794.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.101564 restraints weight = 9688.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7638  Z= 0.257
  Angle     :  0.650  13.469  10408  Z= 0.323
  Chirality :  0.043   0.292   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.869  54.253   1145
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 26.82 %
    Favored  : 67.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.27), residues: 1006
  helix:  0.64 (0.51), residues: 121
  sheet: -1.93 (0.25), residues: 419
  loop : -1.66 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP R 165 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.014   0.002   PHE A3038 
 TYR   0.020   0.002   TYR A2889 
 ARG   0.004   0.001   ARG N  45 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 99
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A 2843 MET cc_start: 0.7970 (tmm) cc_final: 0.7178 (tmm)
REVERT: A 2844 LEU cc_start: 0.7331 (mm) cc_final: 0.7042 (mp)
REVERT: A 2933 CYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6120 (m)
REVERT: A 3126 LEU cc_start: 0.7885 (tp) cc_final: 0.7653 (tp)
REVERT: A 3166 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8226 (tptp)
REVERT: B  360 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6472 (tt0)
REVERT: B  464 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7785 (mp0)
REVERT: H  108 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.6935 (m-80)
  outliers start: 46
  outliers final: 33
  residues processed: 134
  average time/residue: 0.1751
  time to fit residues: 32.6794
Evaluate side-chains
  127 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 89
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3353 ASN
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 74 optimal weight:    0.4980
   chunk 60 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0370
   chunk 64 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A3099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.112299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.098661 restraints weight = 23131.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.100319 restraints weight = 13749.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.101411 restraints weight = 9651.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7638  Z= 0.255
  Angle     :  0.640  10.560  10408  Z= 0.321
  Chirality :  0.043   0.288   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.902  54.387   1145
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 27.08 %
    Favored  : 66.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.27), residues: 1006
  helix:  0.70 (0.53), residues: 116
  sheet: -1.98 (0.25), residues: 424
  loop : -1.63 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.011   0.001   PHE B 424 
 TYR   0.022   0.002   TYR B 342 
 ARG   0.002   0.000   ARG B 345 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 97
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8060 (tmm) cc_final: 0.7295 (tmm)
REVERT: A 2844 LEU cc_start: 0.7456 (mm) cc_final: 0.7164 (mp)
REVERT: A 2933 CYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6085 (m)
REVERT: A 3126 LEU cc_start: 0.7936 (tp) cc_final: 0.7685 (tp)
REVERT: A 3166 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8153 (tptp)
REVERT: B  360 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6468 (tt0)
REVERT: B  464 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7801 (mp0)
REVERT: H   79 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8311 (tp)
REVERT: H  108 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6740 (m-80)
  outliers start: 49
  outliers final: 34
  residues processed: 134
  average time/residue: 0.1742
  time to fit residues: 32.4684
Evaluate side-chains
  131 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 91
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3353 ASN
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 12 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0770
   chunk 86 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.8098

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

Flipped N/Q/H residues before XYZ refinement:
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.111241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.097779 restraints weight = 23164.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.099286 restraints weight = 14285.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.100269 restraints weight = 10293.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   7638  Z= 0.323
  Angle     :  0.681  10.374  10408  Z= 0.344
  Chirality :  0.044   0.294   1204
  Planarity :  0.004   0.051   1357
  Dihedral  :  6.152  54.715   1145
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  7.13 %
    Allowed  : 26.82 %
    Favored  : 66.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.27), residues: 1006
  helix:  0.55 (0.52), residues: 117
  sheet: -2.03 (0.25), residues: 434
  loop : -1.60 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N 113 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.016   0.002   PHE A3038 
 TYR   0.018   0.002   TYR A2889 
 ARG   0.003   0.000   ARG B 345 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 97
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8059 (tmm) cc_final: 0.7297 (tmm)
REVERT: A 2933 CYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5814 (m)
REVERT: A 3166 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8171 (tptp)
REVERT: A 3359 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.4606 (pm20)
REVERT: B  360 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6566 (tt0)
REVERT: B  426 GLU cc_start: 0.6975 (pp20) cc_final: 0.6724 (pp20)
REVERT: B  464 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7896 (mp0)
REVERT: H   79 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8364 (tp)
REVERT: H  108 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6891 (m-80)
  outliers start: 54
  outliers final: 40
  residues processed: 138
  average time/residue: 0.1855
  time to fit residues: 35.5235
Evaluate side-chains
  135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 88
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3353 ASN
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3359 GLN
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   58 LYS
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain L residue   97 TYR
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 41 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0670
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** A3114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.112754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.099153 restraints weight = 23253.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.100747 restraints weight = 13923.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.101842 restraints weight = 9858.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7638  Z= 0.227
  Angle     :  0.646   9.925  10408  Z= 0.322
  Chirality :  0.043   0.267   1204
  Planarity :  0.004   0.050   1357
  Dihedral  :  5.981  57.827   1145
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 28.27 %
    Favored  : 65.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.27), residues: 1006
  helix:  0.62 (0.51), residues: 122
  sheet: -2.00 (0.25), residues: 426
  loop : -1.48 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.018   0.001   PHE B 340 
 TYR   0.024   0.002   TYR B 342 
 ARG   0.002   0.000   ARG A2836 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 103
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8058 (tmm) cc_final: 0.7290 (tmm)
REVERT: A 2844 LEU cc_start: 0.7429 (mm) cc_final: 0.7133 (mp)
REVERT: A 2933 CYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6784 (m)
REVERT: A 3166 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8102 (tptp)
REVERT: B  360 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6521 (tt0)
REVERT: H  108 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6743 (m-80)
REVERT: N    5 GLN cc_start: 0.5576 (OUTLIER) cc_final: 0.4943 (pm20)
  outliers start: 50
  outliers final: 38
  residues processed: 141
  average time/residue: 0.1807
  time to fit residues: 35.3111
Evaluate side-chains
  137 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 94
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0670
   chunk 43 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 69 optimal weight:    0.3980
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A3094 ASN
** A3114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.112298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.098968 restraints weight = 23239.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.100484 restraints weight = 14198.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.101505 restraints weight = 10191.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7638  Z= 0.254
  Angle     :  0.661   9.687  10408  Z= 0.332
  Chirality :  0.043   0.271   1204
  Planarity :  0.004   0.050   1357
  Dihedral  :  5.941  55.018   1145
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 28.40 %
    Favored  : 64.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.27), residues: 1006
  helix:  0.63 (0.51), residues: 122
  sheet: -1.98 (0.25), residues: 428
  loop : -1.47 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP N 113 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.018   0.002   PHE A3038 
 TYR   0.015   0.001   TYR L  55 
 ARG   0.003   0.001   ARG H  99 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 96
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8041 (tmm) cc_final: 0.7338 (tmm)
REVERT: A 2844 LEU cc_start: 0.7403 (mm) cc_final: 0.7122 (mp)
REVERT: A 2933 CYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6782 (m)
REVERT: A 3166 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8100 (tptp)
REVERT: A 3359 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.4570 (pm20)
REVERT: B  360 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6541 (tt0)
REVERT: H   79 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8303 (tp)
REVERT: H  108 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6698 (m-80)
  outliers start: 51
  outliers final: 41
  residues processed: 137
  average time/residue: 0.1639
  time to fit residues: 31.6941
Evaluate side-chains
  138 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 91
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3359 GLN
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0570
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6102

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

Flipped N/Q/H residues before XYZ refinement:
** A3114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.112010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.098387 restraints weight = 23465.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.100002 restraints weight = 13989.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.101124 restraints weight = 9858.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7638  Z= 0.266
  Angle     :  0.673   9.695  10408  Z= 0.339
  Chirality :  0.043   0.267   1204
  Planarity :  0.004   0.050   1357
  Dihedral  :  5.902  55.232   1145
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  7.27 %
    Allowed  : 28.27 %
    Favored  : 64.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.27), residues: 1006
  helix:  0.74 (0.51), residues: 122
  sheet: -1.90 (0.25), residues: 430
  loop : -1.47 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N 113 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.017   0.002   PHE B 340 
 TYR   0.029   0.002   TYR B 342 
 ARG   0.003   0.001   ARG N  67 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 95
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8039 (tmm) cc_final: 0.7371 (tmm)
REVERT: A 2844 LEU cc_start: 0.7445 (mm) cc_final: 0.7169 (mp)
REVERT: A 2933 CYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6640 (m)
REVERT: A 3166 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8116 (tptp)
REVERT: A 3359 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.4587 (pm20)
REVERT: B  360 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6510 (tt0)
REVERT: B  456 LEU cc_start: 0.8629 (mt) cc_final: 0.8391 (mt)
REVERT: B  464 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7841 (mp0)
REVERT: H   79 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8210 (tp)
REVERT: H  108 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6751 (m-80)
REVERT: L   79 LEU cc_start: 0.7667 (tp) cc_final: 0.7022 (pp)
  outliers start: 55
  outliers final: 42
  residues processed: 141
  average time/residue: 0.1645
  time to fit residues: 32.9479
Evaluate side-chains
  142 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 93
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3359 GLN
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  114 PHE
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    0.0870
   chunk 67 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0970
   chunk 54 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
** A3114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.112545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.098990 restraints weight = 23345.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.100657 restraints weight = 13809.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.101728 restraints weight = 9723.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7638  Z= 0.241
  Angle     :  0.679  10.677  10408  Z= 0.340
  Chirality :  0.043   0.262   1204
  Planarity :  0.004   0.050   1357
  Dihedral  :  5.818  55.308   1145
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 29.33 %
    Favored  : 64.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.27), residues: 1006
  helix:  0.89 (0.51), residues: 121
  sheet: -1.81 (0.25), residues: 428
  loop : -1.47 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N 113 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.019   0.002   PHE A3038 
 TYR   0.016   0.001   TYR B 425 
 ARG   0.004   0.001   ARG A2836 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 99
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8040 (tmm) cc_final: 0.7380 (tmm)
REVERT: A 2844 LEU cc_start: 0.7411 (mm) cc_final: 0.7136 (mp)
REVERT: A 2933 CYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6653 (m)
REVERT: A 3166 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8127 (tptp)
REVERT: A 3339 TYR cc_start: 0.7105 (t80) cc_final: 0.6753 (t80)
REVERT: B  464 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7786 (mp0)
REVERT: H   29 PHE cc_start: 0.8094 (t80) cc_final: 0.7835 (t80)
REVERT: H   79 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8265 (tp)
REVERT: H  108 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6715 (m-80)
REVERT: L   79 LEU cc_start: 0.7643 (tp) cc_final: 0.7010 (pp)
REVERT: N    5 GLN cc_start: 0.5065 (OUTLIER) cc_final: 0.4506 (pm20)
REVERT: N   38 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8053 (ttp-170)
  outliers start: 46
  outliers final: 38
  residues processed: 136
  average time/residue: 0.1691
  time to fit residues: 32.3686
Evaluate side-chains
  143 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 98
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 50 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A3114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.110749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.098658 restraints weight = 23424.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.098860 restraints weight = 15923.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.099237 restraints weight = 13752.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   7638  Z= 0.315
  Angle     :  0.714  10.990  10408  Z= 0.362
  Chirality :  0.043   0.270   1204
  Planarity :  0.004   0.052   1357
  Dihedral  :  6.071  55.743   1145
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 28.67 %
    Favored  : 64.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.27), residues: 1006
  helix:  0.73 (0.51), residues: 121
  sheet: -1.87 (0.25), residues: 426
  loop : -1.56 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP N 113 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.016   0.002   PHE B 340 
 TYR   0.016   0.002   TYR L  92 
 ARG   0.003   0.001   ARG A2836 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2645.83 seconds
wall clock time: 46 minutes 36.51 seconds (2796.51 seconds total)