Starting phenix.real_space_refine
on Fri May 16 09:51:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dyh_47304/05_2025/9dyh_47304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dyh_47304/05_2025/9dyh_47304.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dyh_47304/05_2025/9dyh_47304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dyh_47304/05_2025/9dyh_47304.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dyh_47304/05_2025/9dyh_47304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dyh_47304/05_2025/9dyh_47304.cif"
  }
  resolution = 3.15
  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=   0.001 sd=   0.062
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      5      9.91       5
     S      80      5.16       5
     C    9415      2.51       5
     N    2355      2.21       5
     O    2485      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14340
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2867
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 347, 2863
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 9, 'TRANS': 337}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 347, 2863
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 9, 'TRANS': 337}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 2935
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 8.25, per 1000 atoms: 0.58
  Number of scatterers: 14340
  At special positions: 0
  Unit cell: (91.575, 92.4, 108.075, 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      5     19.99
     S      80     16.00
     O    2485      8.00
     N    2355      7.00
     C    9415      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.62
  Conformation dependent library (CDL) restraints added in 3.3 seconds
  

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3290

  Finding SS restraints...
    Secondary structure from input PDB file:
      85 helices and 0 sheets defined
      76.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 10
    Processing helix  chain 'A' and resid 17 through 23
      removed outlier: 3.584A  pdb=" N   LEU A  22 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 53
      removed outlier: 5.654A  pdb=" N   ARG A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   GLU A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 73
    Processing helix  chain 'A' and resid 74 through 76
      No H-bonds generated for 'chain 'A' and resid 74 through 76'
    Processing helix  chain 'A' and resid 77 through 99
    Processing helix  chain 'A' and resid 103 through 114
    Processing helix  chain 'A' and resid 118 through 144
    Processing helix  chain 'A' and resid 144 through 151
    Processing helix  chain 'A' and resid 153 through 160
      removed outlier: 3.503A  pdb=" N   VAL A 157 " --> pdb=" O   THR A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 174
    Processing helix  chain 'A' and resid 182 through 198
    Processing helix  chain 'A' and resid 203 through 230
    Processing helix  chain 'A' and resid 233 through 255
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 274 through 296
      removed outlier: 4.405A  pdb=" N   ASN A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 323
    Processing helix  chain 'E' and resid 6 through 10
    Processing helix  chain 'E' and resid 17 through 23
      removed outlier: 3.584A  pdb=" N   LEU E  22 " --> pdb=" O   GLN E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 53
      removed outlier: 5.654A  pdb=" N   ARG E  34 " --> pdb=" O   LYS E  30 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   GLU E  35 " --> pdb=" O   LEU E  31 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 73
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 77 through 99
    Processing helix  chain 'E' and resid 103 through 114
    Processing helix  chain 'E' and resid 118 through 144
    Processing helix  chain 'E' and resid 144 through 151
    Processing helix  chain 'E' and resid 153 through 160
      removed outlier: 3.504A  pdb=" N   VAL E 157 " --> pdb=" O   THR E 153 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 164 through 174
    Processing helix  chain 'E' and resid 182 through 198
    Processing helix  chain 'E' and resid 203 through 230
    Processing helix  chain 'E' and resid 233 through 255
    Processing helix  chain 'E' and resid 259 through 263
    Processing helix  chain 'E' and resid 274 through 296
      removed outlier: 4.405A  pdb=" N   ASN E 296 " --> pdb=" O   GLU E 292 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 306 through 323
    Processing helix  chain 'D' and resid 6 through 10
    Processing helix  chain 'D' and resid 17 through 23
      removed outlier: 3.584A  pdb=" N   LEU D  22 " --> pdb=" O   GLN D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 27 through 53
      removed outlier: 5.653A  pdb=" N   ARG D  34 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   GLU D  35 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 73
    Processing helix  chain 'D' and resid 74 through 76
      No H-bonds generated for 'chain 'D' and resid 74 through 76'
    Processing helix  chain 'D' and resid 77 through 99
    Processing helix  chain 'D' and resid 103 through 114
    Processing helix  chain 'D' and resid 118 through 144
    Processing helix  chain 'D' and resid 144 through 151
    Processing helix  chain 'D' and resid 153 through 160
      removed outlier: 3.503A  pdb=" N   VAL D 157 " --> pdb=" O   THR D 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 164 through 174
    Processing helix  chain 'D' and resid 182 through 198
    Processing helix  chain 'D' and resid 203 through 230
    Processing helix  chain 'D' and resid 233 through 255
    Processing helix  chain 'D' and resid 259 through 263
    Processing helix  chain 'D' and resid 274 through 296
      removed outlier: 4.405A  pdb=" N   ASN D 296 " --> pdb=" O   GLU D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 323
    Processing helix  chain 'B' and resid 6 through 10
    Processing helix  chain 'B' and resid 17 through 23
      removed outlier: 3.584A  pdb=" N   LEU B  22 " --> pdb=" O   GLN B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 53
      removed outlier: 5.654A  pdb=" N   ARG B  34 " --> pdb=" O   LYS B  30 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   GLU B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 73
    Processing helix  chain 'B' and resid 74 through 76
      No H-bonds generated for 'chain 'B' and resid 74 through 76'
    Processing helix  chain 'B' and resid 77 through 99
    Processing helix  chain 'B' and resid 103 through 114
    Processing helix  chain 'B' and resid 118 through 144
    Processing helix  chain 'B' and resid 144 through 151
    Processing helix  chain 'B' and resid 153 through 160
      removed outlier: 3.503A  pdb=" N   VAL B 157 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 174
    Processing helix  chain 'B' and resid 182 through 198
    Processing helix  chain 'B' and resid 203 through 230
    Processing helix  chain 'B' and resid 233 through 255
    Processing helix  chain 'B' and resid 259 through 263
    Processing helix  chain 'B' and resid 274 through 296
      removed outlier: 4.405A  pdb=" N   ASN B 296 " --> pdb=" O   GLU B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 323
    Processing helix  chain 'C' and resid 6 through 10
    Processing helix  chain 'C' and resid 17 through 23
      removed outlier: 3.584A  pdb=" N   LEU C  22 " --> pdb=" O   GLN C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 53
      removed outlier: 5.654A  pdb=" N   ARG C  34 " --> pdb=" O   LYS C  30 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   GLU C  35 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 73
    Processing helix  chain 'C' and resid 74 through 76
      No H-bonds generated for 'chain 'C' and resid 74 through 76'
    Processing helix  chain 'C' and resid 77 through 99
    Processing helix  chain 'C' and resid 103 through 114
    Processing helix  chain 'C' and resid 118 through 144
    Processing helix  chain 'C' and resid 144 through 151
    Processing helix  chain 'C' and resid 153 through 160
      removed outlier: 3.503A  pdb=" N   VAL C 157 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 174
    Processing helix  chain 'C' and resid 182 through 198
    Processing helix  chain 'C' and resid 203 through 230
    Processing helix  chain 'C' and resid 233 through 255
    Processing helix  chain 'C' and resid 259 through 263
    Processing helix  chain 'C' and resid 274 through 296
      removed outlier: 4.406A  pdb=" N   ASN C 296 " --> pdb=" O   GLU C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 323

    975 hydrogen bonds defined for protein.
    2815 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: 4.17

  Time building geometry restraints manager: 4.22 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2549
        1.32 -     1.45: 4164
        1.45 -     1.57: 7892
        1.57 -     1.70: 0
        1.70 -     1.83: 120
  Bond restraints: 14725
  Sorted by residual:
  bond pdb=" CA  VAL C 183 "
       pdb=" CB  VAL C 183 "
    ideal  model  delta    sigma   weight residual
    1.539  1.518  0.021 5.40e-03 3.43e+04 1.58e+01
  bond pdb=" CA  VAL D 183 "
       pdb=" CB  VAL D 183 "
    ideal  model  delta    sigma   weight residual
    1.539  1.518  0.021 5.40e-03 3.43e+04 1.58e+01
  bond pdb=" CA  VAL A 183 "
       pdb=" CB  VAL A 183 "
    ideal  model  delta    sigma   weight residual
    1.539  1.518  0.021 5.40e-03 3.43e+04 1.56e+01
  bond pdb=" CA  VAL B 183 "
       pdb=" CB  VAL B 183 "
    ideal  model  delta    sigma   weight residual
    1.539  1.518  0.021 5.40e-03 3.43e+04 1.47e+01
  bond pdb=" CA  VAL E 183 "
       pdb=" CB  VAL E 183 "
    ideal  model  delta    sigma   weight residual
    1.539  1.518  0.021 5.40e-03 3.43e+04 1.47e+01
  ... (remaining 14720 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 12659
        1.27 -     2.54: 6101
        2.54 -     3.81: 1126
        3.81 -     5.07: 77
        5.07 -     6.34: 17
  Bond angle restraints: 19980
  Sorted by residual:
  angle pdb=" N   THR D 277 "
        pdb=" CA  THR D 277 "
        pdb=" C   THR D 277 "
      ideal   model   delta    sigma   weight residual
     111.28  104.94    6.34 1.09e+00 8.42e-01 3.39e+01
  angle pdb=" N   THR B 277 "
        pdb=" CA  THR B 277 "
        pdb=" C   THR B 277 "
      ideal   model   delta    sigma   weight residual
     111.28  104.95    6.33 1.09e+00 8.42e-01 3.37e+01
  angle pdb=" N   THR A 277 "
        pdb=" CA  THR A 277 "
        pdb=" C   THR A 277 "
      ideal   model   delta    sigma   weight residual
     111.28  104.97    6.31 1.09e+00 8.42e-01 3.35e+01
  angle pdb=" N   THR C 277 "
        pdb=" CA  THR C 277 "
        pdb=" C   THR C 277 "
      ideal   model   delta    sigma   weight residual
     111.28  104.98    6.30 1.09e+00 8.42e-01 3.34e+01
  angle pdb=" N   THR E 277 "
        pdb=" CA  THR E 277 "
        pdb=" C   THR E 277 "
      ideal   model   delta    sigma   weight residual
     111.28  105.02    6.26 1.09e+00 8.42e-01 3.30e+01
  ... (remaining 19975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.16: 7480
       16.16 -    32.33: 720
       32.33 -    48.49: 240
       48.49 -    64.66: 55
       64.66 -    80.82: 20
  Dihedral angle restraints: 8515
    sinusoidal: 3385
      harmonic: 5130
  Sorted by residual:
  dihedral pdb=" CA  LEU E 329 "
           pdb=" C   LEU E 329 "
           pdb=" N   ALA E 330 "
           pdb=" CA  ALA E 330 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.46   19.54     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  LEU C 329 "
           pdb=" C   LEU C 329 "
           pdb=" N   ALA C 330 "
           pdb=" CA  ALA C 330 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.47   19.53     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  LEU A 329 "
           pdb=" C   LEU A 329 "
           pdb=" N   ALA A 330 "
           pdb=" CA  ALA A 330 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.48   19.52     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 8512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 886
       0.039 -    0.078: 616
       0.078 -    0.117: 460
       0.117 -    0.156: 157
       0.156 -    0.195: 51
  Chirality restraints: 2170
  Sorted by residual:
  chirality pdb=" CB  ILE E  28 "
            pdb=" CA  ILE E  28 "
            pdb=" CG1 ILE E  28 "
            pdb=" CG2 ILE E  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.52e-01
  chirality pdb=" CA  VAL E   3 "
            pdb=" N   VAL E   3 "
            pdb=" C   VAL E   3 "
            pdb=" CB  VAL E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.19 2.00e-01 2.50e+01 9.47e-01
  chirality pdb=" CB  ILE A  28 "
            pdb=" CA  ILE A  28 "
            pdb=" CG1 ILE A  28 "
            pdb=" CG2 ILE A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.39e-01
  ... (remaining 2167 not shown)

  Planarity restraints: 2495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 182 "   -0.038 2.00e-02 2.50e+03   2.12e-02 1.12e+01
        pdb=" CG  TRP A 182 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 182 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 182 "    0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 182 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 182 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 182 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 182 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 182 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 182 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 182 "    0.038 2.00e-02 2.50e+03   2.12e-02 1.12e+01
        pdb=" CG  TRP B 182 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 182 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 182 "   -0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 182 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 182 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 182 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 182 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 182 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 182 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 182 "   -0.038 2.00e-02 2.50e+03   2.12e-02 1.12e+01
        pdb=" CG  TRP D 182 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 182 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 182 "    0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 182 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 182 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 182 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 182 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 182 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 182 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 2492 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 113
        2.57 -     3.16: 11945
        3.16 -     3.74: 24722
        3.74 -     4.32: 35265
        4.32 -     4.90: 55616
  Nonbonded interactions: 127661
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 237 "
            pdb=" OH  TYR D   5 "
     model   vdw
     1.993 3.040
  nonbonded pdb=" OH  TYR A   5 "
            pdb=" OG1 THR B 237 "
     model   vdw
     2.004 3.040
  nonbonded pdb=" OG1 THR A 237 "
            pdb=" OH  TYR E   5 "
     model   vdw
     2.011 3.040
  nonbonded pdb=" OH  TYR B   5 "
            pdb=" OG1 THR C 237 "
     model   vdw
     2.012 3.040
  nonbonded pdb=" OG1 THR D 237 "
            pdb=" OH  TYR C   5 "
     model   vdw
     2.018 3.040
  ... (remaining 127656 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             3.010
  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:          0.600
  Check model and map are aligned:         0.100
  Set scattering table:                    0.150
  Process input model:                     35.270
  Find NCS groups from input model:        0.300
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
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      :  0.012   0.058  14725  Z= 0.896
  Angle     :  1.367   6.343  19980  Z= 1.053
  Chirality :  0.072   0.195   2170
  Planarity :  0.006   0.023   2495
  Dihedral  : 15.273  80.825   5225
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.87 %
    Favored  : 88.49 %
  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:  1.20 (0.19), residues: 1710
  helix:  1.32 (0.14), residues: 1190
  sheet:  None (None), residues: 0
  loop : -0.28 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.010   TRP A 182 
 HIS   0.005   0.002   HIS A 115 
 PHE   0.035   0.007   PHE E 171 
 TYR   0.045   0.009   TYR D 124 
 ARG   0.013   0.002   ARG C 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13785 (  975)
  hydrogen bonds       : angle       5.13391 ( 2815)
  covalent geometry    : bond        0.01227 (14725)
  covalent geometry    : angle       1.36702 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  482 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 457
  time to evaluate  : 1.483 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8453 (tp) cc_final: 0.8188 (tt)
REVERT: A   34 ARG cc_start: 0.6764 (mtt90) cc_final: 0.6081 (mtm180)
REVERT: A   58 GLN cc_start: 0.6960 (mt0) cc_final: 0.6635 (mt0)
REVERT: A   63 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7119 (mt-10)
REVERT: A   71 GLN cc_start: 0.7154 (tt0) cc_final: 0.6172 (mm110)
REVERT: A   91 ASN cc_start: 0.8531 (m-40) cc_final: 0.8171 (m110)
REVERT: A  197 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.8086 (ttm-80)
REVERT: A  249 LEU cc_start: 0.7236 (mt) cc_final: 0.7030 (mp)
REVERT: E   29 TYR cc_start: 0.8312 (m-80) cc_final: 0.8061 (m-80)
REVERT: E   34 ARG cc_start: 0.6879 (mtt90) cc_final: 0.6230 (mtm180)
REVERT: E   71 GLN cc_start: 0.7409 (tt0) cc_final: 0.7166 (tt0)
REVERT: E  170 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6314 (mtmt)
REVERT: E  197 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.8032 (ttm-80)
REVERT: E  202 ARG cc_start: 0.7793 (mtt180) cc_final: 0.7420 (mtp-110)
REVERT: D   32 LEU cc_start: 0.8053 (tp) cc_final: 0.7630 (tt)
REVERT: D   34 ARG cc_start: 0.7053 (mtt90) cc_final: 0.6256 (mtm180)
REVERT: D   63 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7125 (mp0)
REVERT: D   91 ASN cc_start: 0.8752 (m-40) cc_final: 0.8439 (m110)
REVERT: D  149 LYS cc_start: 0.8256 (mttp) cc_final: 0.8009 (mttt)
REVERT: D  166 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8129 (mm-30)
REVERT: D  170 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6626 (mtpt)
REVERT: D  197 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.8059 (ttm-80)
REVERT: D  202 ARG cc_start: 0.8121 (mtt180) cc_final: 0.7334 (mtp-110)
REVERT: D  249 LEU cc_start: 0.7409 (mt) cc_final: 0.7119 (mp)
REVERT: D  306 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7326 (mm-30)
REVERT: D  316 GLN cc_start: 0.8088 (tm130) cc_final: 0.7608 (tt0)
REVERT: D  336 LEU cc_start: 0.6930 (tp) cc_final: 0.6695 (tp)
REVERT: B   14 PHE cc_start: 0.7598 (t80) cc_final: 0.7066 (t80)
REVERT: B   32 LEU cc_start: 0.8321 (tp) cc_final: 0.7941 (tt)
REVERT: B   38 CYS cc_start: 0.8077 (m) cc_final: 0.7598 (t)
REVERT: B  170 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6742 (mtmt)
REVERT: B  213 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6826 (mm-30)
REVERT: B  276 PHE cc_start: 0.6674 (m-80) cc_final: 0.6404 (m-80)
REVERT: B  282 PHE cc_start: 0.7726 (t80) cc_final: 0.7171 (t80)
REVERT: B  325 MET cc_start: 0.8073 (mtp) cc_final: 0.7731 (mtp)
REVERT: C   34 ARG cc_start: 0.7153 (mtt90) cc_final: 0.6527 (mtm180)
REVERT: C  202 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7234 (mtp-110)
REVERT: C  282 PHE cc_start: 0.7640 (t80) cc_final: 0.7373 (t80)
  outliers start: 25
  outliers final: 0
  residues processed: 468
  average time/residue: 0.2905
  time to fit residues: 190.4553
Evaluate side-chains
  240 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 237
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  170 LYS
Chi-restraints excluded: chain D residue  170 LYS
Chi-restraints excluded: chain B residue  170 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    0.7980
   chunk 128 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 133 optimal weight:    0.9990
   chunk 51 optimal weight:    0.2980
   chunk 81 optimal weight:    0.5980
   chunk 99 optimal weight:    0.6980
   chunk 154 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 173 ASN
A 316 GLN
A 361 GLN
E 316 GLN
E 361 GLN
** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 173 ASN
D 361 GLN
B  91 ASN
B 238 GLN
B 361 GLN
C  96 GLN
** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 204 ASN
C 361 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.168504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.149655 restraints weight = 37864.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 3.00
r_work: 0.3581 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14725  Z= 0.164
  Angle     :  0.614  11.275  19980  Z= 0.325
  Chirality :  0.042   0.183   2170
  Planarity :  0.004   0.048   2495
  Dihedral  :  4.628  40.436   1972
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.43 %
    Favored  : 85.72 %
  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:  1.28 (0.20), residues: 1710
  helix:  1.28 (0.14), residues: 1235
  sheet:  None (None), residues: 0
  loop : -0.13 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  94 
 HIS   0.002   0.001   HIS A 267 
 PHE   0.039   0.002   PHE E  42 
 TYR   0.030   0.002   TYR D  43 
 ARG   0.012   0.001   ARG A 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05792 (  975)
  hydrogen bonds       : angle       4.77468 ( 2815)
  covalent geometry    : bond        0.00346 (14725)
  covalent geometry    : angle       0.61429 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 265
  time to evaluate  : 1.712 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7422 (mtt90) cc_final: 0.7168 (mtm180)
REVERT: A   71 GLN cc_start: 0.6863 (tt0) cc_final: 0.5942 (mm110)
REVERT: A   91 ASN cc_start: 0.8990 (m-40) cc_final: 0.8542 (m110)
REVERT: E   19 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6611 (mm110)
REVERT: E   34 ARG cc_start: 0.7424 (mtt90) cc_final: 0.6865 (mtm180)
REVERT: E   44 MET cc_start: 0.7367 (mmm) cc_final: 0.6832 (mmm)
REVERT: E  202 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7283 (mtp-110)
REVERT: E  306 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6937 (mp0)
REVERT: E  324 GLU cc_start: 0.8093 (tp30) cc_final: 0.7736 (tm-30)
REVERT: D   19 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6186 (mm110)
REVERT: D   91 ASN cc_start: 0.8933 (m-40) cc_final: 0.8591 (m110)
REVERT: D  149 LYS cc_start: 0.8472 (mttp) cc_final: 0.8197 (mttt)
REVERT: D  202 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7327 (mtp-110)
REVERT: D  245 TYR cc_start: 0.7436 (m-10) cc_final: 0.7178 (m-80)
REVERT: D  306 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7239 (mp0)
REVERT: D  316 GLN cc_start: 0.8328 (tm130) cc_final: 0.7701 (tt0)
REVERT: B   32 LEU cc_start: 0.8480 (tp) cc_final: 0.8177 (tt)
REVERT: B   36 LEU cc_start: 0.8706 (tp) cc_final: 0.8436 (mp)
REVERT: B  173 ASN cc_start: 0.8148 (m-40) cc_final: 0.7890 (m-40)
REVERT: C   34 ARG cc_start: 0.7723 (mtt90) cc_final: 0.7410 (mtm180)
REVERT: C  168 ARG cc_start: 0.7291 (tmt90) cc_final: 0.6898 (tmm-80)
REVERT: C  173 ASN cc_start: 0.7601 (m-40) cc_final: 0.7391 (m110)
REVERT: C  202 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7163 (mtp-110)
REVERT: C  282 PHE cc_start: 0.7934 (t80) cc_final: 0.7677 (t80)
  outliers start: 28
  outliers final: 11
  residues processed: 288
  average time/residue: 0.2839
  time to fit residues: 118.8977
Evaluate side-chains
  235 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 222
  time to evaluate  : 1.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain E residue   19 GLN
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain D residue   19 GLN
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  177 SER
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue  177 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 104 optimal weight:    0.0970
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 169 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 173 ASN
E 156 HIS
E 204 ASN
D 156 HIS
D 173 ASN
B  91 ASN
B 115 HIS
C 156 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.164663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.147131 restraints weight = 31259.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.57
r_work: 0.3546 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14725  Z= 0.174
  Angle     :  0.590   8.832  19980  Z= 0.316
  Chirality :  0.042   0.188   2170
  Planarity :  0.004   0.056   2495
  Dihedral  :  4.118  18.689   1960
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 13.36 %
    Favored  : 84.80 %
  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:  1.19 (0.20), residues: 1710
  helix:  1.21 (0.14), residues: 1235
  sheet:  None (None), residues: 0
  loop : -0.15 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 182 
 HIS   0.002   0.001   HIS A 267 
 PHE   0.052   0.002   PHE E  42 
 TYR   0.026   0.002   TYR A  97 
 ARG   0.011   0.001   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05534 (  975)
  hydrogen bonds       : angle       4.76685 ( 2815)
  covalent geometry    : bond        0.00382 (14725)
  covalent geometry    : angle       0.58958 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 252
  time to evaluate  : 1.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7557 (mtt90) cc_final: 0.7240 (mtm180)
REVERT: A   38 CYS cc_start: 0.7679 (p) cc_final: 0.7464 (p)
REVERT: E   19 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6176 (mm110)
REVERT: E   44 MET cc_start: 0.7045 (mmm) cc_final: 0.6791 (mmm)
REVERT: E  324 GLU cc_start: 0.8253 (tp30) cc_final: 0.7912 (tm-30)
REVERT: D   19 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6176 (mm110)
REVERT: D   32 LEU cc_start: 0.8390 (tp) cc_final: 0.8180 (tt)
REVERT: D  149 LYS cc_start: 0.8504 (mttp) cc_final: 0.8238 (mttt)
REVERT: D  173 ASN cc_start: 0.7921 (m-40) cc_final: 0.7698 (m-40)
REVERT: D  202 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7465 (mtp-110)
REVERT: D  218 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7500 (ttp80)
REVERT: B   32 LEU cc_start: 0.8407 (tp) cc_final: 0.8054 (tt)
REVERT: B  173 ASN cc_start: 0.8206 (m-40) cc_final: 0.7939 (m-40)
REVERT: C   34 ARG cc_start: 0.7814 (mtt90) cc_final: 0.7506 (mtm180)
REVERT: C  202 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7245 (mtp-110)
  outliers start: 28
  outliers final: 15
  residues processed: 273
  average time/residue: 0.2784
  time to fit residues: 112.2887
Evaluate side-chains
  231 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 214
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain E residue   19 GLN
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain D residue   19 GLN
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  177 SER
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue  177 SER
Chi-restraints excluded: chain C residue  214 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 76 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 115 HIS
** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 173 ASN
E 204 ASN
D  91 ASN
D 204 ASN
B  96 GLN
B 204 ASN
C 173 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.161997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.142915 restraints weight = 41132.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 3.03
r_work: 0.3489 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3526
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14725  Z= 0.184
  Angle     :  0.599  11.138  19980  Z= 0.321
  Chirality :  0.042   0.189   2170
  Planarity :  0.004   0.052   2495
  Dihedral  :  4.117  18.971   1960
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.41 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.20), residues: 1710
  helix:  1.12 (0.14), residues: 1235
  sheet:  None (None), residues: 0
  loop : -0.14 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E  33 
 HIS   0.004   0.001   HIS D 156 
 PHE   0.050   0.002   PHE E  42 
 TYR   0.024   0.002   TYR A  43 
 ARG   0.011   0.001   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05478 (  975)
  hydrogen bonds       : angle       4.78044 ( 2815)
  covalent geometry    : bond        0.00415 (14725)
  covalent geometry    : angle       0.59875 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 236
  time to evaluate  : 1.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 CYS cc_start: 0.7737 (p) cc_final: 0.7066 (p)
REVERT: A  202 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7604 (mtp180)
REVERT: A  203 ASP cc_start: 0.7211 (p0) cc_final: 0.6734 (m-30)
REVERT: A  319 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7362 (mmp)
REVERT: E   19 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6124 (mm110)
REVERT: E   44 MET cc_start: 0.7070 (mmm) cc_final: 0.6771 (mmm)
REVERT: E  324 GLU cc_start: 0.8305 (tp30) cc_final: 0.8038 (tm-30)
REVERT: D   19 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6213 (mm110)
REVERT: D   32 LEU cc_start: 0.8401 (tp) cc_final: 0.8173 (tt)
REVERT: D  149 LYS cc_start: 0.8481 (mttp) cc_final: 0.8240 (mttt)
REVERT: D  202 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7549 (mtp-110)
REVERT: D  218 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7533 (ttp80)
REVERT: B  173 ASN cc_start: 0.8265 (m-40) cc_final: 0.7949 (m-40)
REVERT: B  218 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7191 (ttp80)
REVERT: C   34 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7555 (mtm180)
REVERT: C   91 ASN cc_start: 0.8627 (m110) cc_final: 0.8300 (m110)
REVERT: C  202 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7370 (mtp-110)
  outliers start: 26
  outliers final: 19
  residues processed: 257
  average time/residue: 0.2591
  time to fit residues: 99.3167
Evaluate side-chains
  238 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 216
  time to evaluate  : 1.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain E residue   19 GLN
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain D residue   19 GLN
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  177 SER
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain C residue  177 SER
Chi-restraints excluded: chain C residue  214 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 152 optimal weight:    4.9990
   chunk 126 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 137 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0870
   chunk 34 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.9962

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 204 ASN
D 115 HIS
D 173 ASN
D 204 ASN
C 204 ASN
C 293 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.160043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.140859 restraints weight = 37289.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 3.06
r_work: 0.3499 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3494
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14725  Z= 0.178
  Angle     :  0.590  11.859  19980  Z= 0.317
  Chirality :  0.042   0.208   2170
  Planarity :  0.004   0.041   2495
  Dihedral  :  4.097  19.211   1960
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.93 %
    Favored  : 83.09 %
  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:  1.09 (0.20), residues: 1710
  helix:  1.13 (0.14), residues: 1235
  sheet:  None (None), residues: 0
  loop : -0.14 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  94 
 HIS   0.004   0.001   HIS D 156 
 PHE   0.052   0.002   PHE E  42 
 TYR   0.026   0.002   TYR A  43 
 ARG   0.010   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05376 (  975)
  hydrogen bonds       : angle       4.79816 ( 2815)
  covalent geometry    : bond        0.00399 (14725)
  covalent geometry    : angle       0.58999 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 237
  time to evaluate  : 1.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ASP cc_start: 0.7225 (p0) cc_final: 0.6591 (m-30)
REVERT: E   19 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6855 (pp30)
REVERT: E   44 MET cc_start: 0.6775 (mmm) cc_final: 0.6444 (mmm)
REVERT: E   63 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7621 (mp0)
REVERT: E  324 GLU cc_start: 0.8166 (tp30) cc_final: 0.7920 (tm-30)
REVERT: D   19 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6060 (mm110)
REVERT: D   32 LEU cc_start: 0.8238 (tp) cc_final: 0.7927 (tt)
REVERT: D  149 LYS cc_start: 0.8201 (mttp) cc_final: 0.7873 (mttt)
REVERT: D  202 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7501 (mtp-110)
REVERT: D  218 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7348 (ttp80)
REVERT: B  173 ASN cc_start: 0.8066 (m-40) cc_final: 0.7713 (m-40)
REVERT: C   34 ARG cc_start: 0.7498 (mtt90) cc_final: 0.7101 (mtm180)
REVERT: C   91 ASN cc_start: 0.8637 (m110) cc_final: 0.8243 (m110)
REVERT: C  197 ARG cc_start: 0.8467 (ttp80) cc_final: 0.7930 (ttp80)
REVERT: C  202 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7370 (mtp-110)
  outliers start: 30
  outliers final: 20
  residues processed: 262
  average time/residue: 0.2537
  time to fit residues: 99.6953
Evaluate side-chains
  238 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 215
  time to evaluate  : 1.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain E residue   19 GLN
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   63 GLU
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain D residue   19 GLN
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  177 SER
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain C residue  177 SER
Chi-restraints excluded: chain C residue  214 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 147 optimal weight:    6.9990
   chunk 158 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 140 optimal weight:    1.9990
   chunk 165 optimal weight:    2.9990
   chunk 125 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 173 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.161875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.143777 restraints weight = 36164.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.78
r_work: 0.3504 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14725  Z= 0.165
  Angle     :  0.585  11.659  19980  Z= 0.314
  Chirality :  0.042   0.206   2170
  Planarity :  0.004   0.053   2495
  Dihedral  :  4.078  18.663   1960
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.13 %
    Favored  : 83.09 %
  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:  1.09 (0.20), residues: 1710
  helix:  1.14 (0.14), residues: 1235
  sheet:  None (None), residues: 0
  loop : -0.18 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  93 
 HIS   0.004   0.001   HIS E 115 
 PHE   0.051   0.002   PHE B  42 
 TYR   0.024   0.002   TYR A  43 
 ARG   0.013   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05261 (  975)
  hydrogen bonds       : angle       4.80172 ( 2815)
  covalent geometry    : bond        0.00364 (14725)
  covalent geometry    : angle       0.58488 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 234
  time to evaluate  : 1.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7953 (mtp85)
REVERT: A   38 CYS cc_start: 0.7868 (p) cc_final: 0.7638 (p)
REVERT: A  202 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7725 (mtp85)
REVERT: A  203 ASP cc_start: 0.7156 (p0) cc_final: 0.6831 (m-30)
REVERT: A  249 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7455 (mp)
REVERT: E   19 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6202 (mm110)
REVERT: E   44 MET cc_start: 0.7059 (mmm) cc_final: 0.6745 (mmm)
REVERT: E   63 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7770 (mp0)
REVERT: E  324 GLU cc_start: 0.8158 (tp30) cc_final: 0.7939 (tm-30)
REVERT: D   19 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6518 (mm110)
REVERT: D   32 LEU cc_start: 0.8398 (tp) cc_final: 0.8157 (tt)
REVERT: D  149 LYS cc_start: 0.8483 (mttp) cc_final: 0.8161 (mttt)
REVERT: D  202 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7650 (mtp-110)
REVERT: D  273 VAL cc_start: 0.6678 (t) cc_final: 0.6427 (p)
REVERT: D  316 GLN cc_start: 0.8221 (tt0) cc_final: 0.7985 (tt0)
REVERT: B  173 ASN cc_start: 0.8213 (m-40) cc_final: 0.7884 (m-40)
REVERT: C   34 ARG cc_start: 0.7792 (mtt90) cc_final: 0.7465 (mtm180)
REVERT: C   44 MET cc_start: 0.7235 (mmm) cc_final: 0.6755 (mmp)
REVERT: C   91 ASN cc_start: 0.8656 (m110) cc_final: 0.8272 (m110)
REVERT: C  202 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7561 (mtp-110)
  outliers start: 27
  outliers final: 18
  residues processed: 259
  average time/residue: 0.2689
  time to fit residues: 103.4736
Evaluate side-chains
  246 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 224
  time to evaluate  : 1.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain E residue   19 GLN
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   63 GLU
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain D residue   19 GLN
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  177 SER
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain C residue  177 SER
Chi-restraints excluded: chain C residue  214 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 157 optimal weight:    0.9990
   chunk 148 optimal weight:    2.9990
   chunk 145 optimal weight:    0.7980
   chunk 107 optimal weight:    0.5980
   chunk 101 optimal weight:    3.9990
   chunk 169 optimal weight:    0.0060
   chunk 96 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0020
   chunk 155 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.4604

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 115 HIS
E 314 ASN
D 173 ASN
D 204 ASN
C 204 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.165330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.146017 restraints weight = 43435.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 3.15
r_work: 0.3539 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3539
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14725  Z= 0.137
  Angle     :  0.565  11.955  19980  Z= 0.304
  Chirality :  0.040   0.217   2170
  Planarity :  0.004   0.050   2495
  Dihedral  :  3.994  17.509   1960
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.86 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.20), residues: 1710
  helix:  1.35 (0.14), residues: 1215
  sheet:  None (None), residues: 0
  loop : -0.26 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  94 
 HIS   0.003   0.001   HIS D 156 
 PHE   0.051   0.002   PHE B  42 
 TYR   0.022   0.002   TYR A  43 
 ARG   0.013   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05003 (  975)
  hydrogen bonds       : angle       4.72683 ( 2815)
  covalent geometry    : bond        0.00285 (14725)
  covalent geometry    : angle       0.56499 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 240
  time to evaluate  : 1.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7486 (mtt90) cc_final: 0.7153 (mtm180)
REVERT: A   38 CYS cc_start: 0.7909 (p) cc_final: 0.7702 (p)
REVERT: A  202 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7716 (mtp85)
REVERT: A  203 ASP cc_start: 0.7134 (p0) cc_final: 0.6833 (m-30)
REVERT: A  249 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7454 (mp)
REVERT: E   19 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6140 (mm110)
REVERT: E   44 MET cc_start: 0.7021 (mmm) cc_final: 0.6704 (mmm)
REVERT: E   63 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7780 (mp0)
REVERT: E  324 GLU cc_start: 0.8171 (tp30) cc_final: 0.7966 (tm-30)
REVERT: D   19 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6417 (mm110)
REVERT: D   32 LEU cc_start: 0.8398 (tp) cc_final: 0.8182 (tt)
REVERT: D  149 LYS cc_start: 0.8490 (mttp) cc_final: 0.8166 (mttt)
REVERT: D  273 VAL cc_start: 0.6571 (t) cc_final: 0.6255 (p)
REVERT: B  173 ASN cc_start: 0.8210 (m-40) cc_final: 0.7877 (m-40)
REVERT: B  282 PHE cc_start: 0.7993 (t80) cc_final: 0.7720 (t80)
REVERT: C   34 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7391 (mtm180)
REVERT: C   44 MET cc_start: 0.7304 (mmm) cc_final: 0.6804 (mmp)
REVERT: C  316 GLN cc_start: 0.8305 (tp40) cc_final: 0.7880 (tt0)
  outliers start: 23
  outliers final: 15
  residues processed: 258
  average time/residue: 0.2571
  time to fit residues: 98.4923
Evaluate side-chains
  240 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 221
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain E residue   19 GLN
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   63 GLU
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain D residue   19 GLN
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue  177 SER
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  272 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 128 optimal weight:    0.2980
   chunk 32 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 156 HIS
E 190 ASN
D 173 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.161397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.143827 restraints weight = 29370.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.65
r_work: 0.3541 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14725  Z= 0.170
  Angle     :  0.607  12.341  19980  Z= 0.321
  Chirality :  0.042   0.201   2170
  Planarity :  0.004   0.048   2495
  Dihedral  :  4.040  18.749   1960
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.05 %
    Favored  : 82.24 %
  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:  1.19 (0.20), residues: 1710
  helix:  1.22 (0.14), residues: 1235
  sheet:  None (None), residues: 0
  loop : -0.18 (0.31), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  94 
 HIS   0.003   0.001   HIS D 156 
 PHE   0.055   0.002   PHE B  42 
 TYR   0.025   0.002   TYR A  43 
 ARG   0.012   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05189 (  975)
  hydrogen bonds       : angle       4.76537 ( 2815)
  covalent geometry    : bond        0.00379 (14725)
  covalent geometry    : angle       0.60732 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 231
  time to evaluate  : 1.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7208 (mtt90) cc_final: 0.6778 (mtm180)
REVERT: A  202 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7704 (mtp85)
REVERT: A  203 ASP cc_start: 0.7198 (p0) cc_final: 0.6721 (m-30)
REVERT: A  249 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7170 (mp)
REVERT: E   44 MET cc_start: 0.6799 (mmm) cc_final: 0.6460 (mmm)
REVERT: E   63 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7715 (mp0)
REVERT: E  100 MET cc_start: 0.8291 (ttm) cc_final: 0.8017 (mtp)
REVERT: E  203 ASP cc_start: 0.7439 (p0) cc_final: 0.7218 (p0)
REVERT: E  324 GLU cc_start: 0.8051 (tp30) cc_final: 0.7808 (tm-30)
REVERT: D   19 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6495 (mm110)
REVERT: D   32 LEU cc_start: 0.8261 (tp) cc_final: 0.7975 (tt)
REVERT: D  149 LYS cc_start: 0.8167 (mttp) cc_final: 0.7850 (mttt)
REVERT: D  273 VAL cc_start: 0.6596 (t) cc_final: 0.6317 (p)
REVERT: D  316 GLN cc_start: 0.8156 (tt0) cc_final: 0.7818 (tt0)
REVERT: D  319 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7434 (mmt)
REVERT: D  339 ASP cc_start: 0.6359 (m-30) cc_final: 0.6144 (m-30)
REVERT: B  173 ASN cc_start: 0.8068 (m-40) cc_final: 0.7690 (m-40)
REVERT: B  282 PHE cc_start: 0.7833 (t80) cc_final: 0.7455 (t80)
REVERT: C   34 ARG cc_start: 0.7357 (mtt90) cc_final: 0.7070 (mtm180)
REVERT: C   44 MET cc_start: 0.7074 (mmm) cc_final: 0.6573 (mmp)
REVERT: C  316 GLN cc_start: 0.8300 (tp40) cc_final: 0.7727 (tt0)
  outliers start: 26
  outliers final: 15
  residues processed: 252
  average time/residue: 0.2496
  time to fit residues: 94.8457
Evaluate side-chains
  242 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 223
  time to evaluate  : 1.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   63 GLU
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain D residue   19 GLN
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  177 SER
Chi-restraints excluded: chain D residue  319 MET
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue  177 SER
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  272 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 138 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 149 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 137 optimal weight:    0.4980
   chunk 125 optimal weight:    0.8980
   chunk 155 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 ASN
E 190 ASN
E 314 ASN
D 173 ASN
** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 204 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.163089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.144957 restraints weight = 32309.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.84
r_work: 0.3554 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3547
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3547 r_free = 0.3547    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3547 r_free = 0.3547    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14725  Z= 0.149
  Angle     :  0.599  13.116  19980  Z= 0.316
  Chirality :  0.041   0.215   2170
  Planarity :  0.004   0.045   2495
  Dihedral  :  4.004  17.832   1960
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 16.64 %
    Favored  : 82.11 %
  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:  1.25 (0.20), residues: 1710
  helix:  1.27 (0.14), residues: 1235
  sheet:  None (None), residues: 0
  loop : -0.17 (0.31), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  94 
 HIS   0.003   0.001   HIS D 156 
 PHE   0.054   0.002   PHE B  42 
 TYR   0.024   0.002   TYR A  43 
 ARG   0.012   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05065 (  975)
  hydrogen bonds       : angle       4.75814 ( 2815)
  covalent geometry    : bond        0.00324 (14725)
  covalent geometry    : angle       0.59904 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 232
  time to evaluate  : 1.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7269 (mtt90) cc_final: 0.6736 (mtm180)
REVERT: A   42 PHE cc_start: 0.7326 (m-80) cc_final: 0.6874 (m-80)
REVERT: A  202 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7682 (mtp85)
REVERT: A  203 ASP cc_start: 0.7125 (p0) cc_final: 0.6728 (m-30)
REVERT: A  249 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7181 (mp)
REVERT: E   44 MET cc_start: 0.6799 (mmm) cc_final: 0.6470 (mmm)
REVERT: E   63 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7746 (mp0)
REVERT: E  324 GLU cc_start: 0.8054 (tp30) cc_final: 0.7836 (tm-30)
REVERT: D   19 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6355 (mm110)
REVERT: D   32 LEU cc_start: 0.8226 (tp) cc_final: 0.7943 (tt)
REVERT: D  149 LYS cc_start: 0.8173 (mttp) cc_final: 0.7851 (mttt)
REVERT: D  273 VAL cc_start: 0.6611 (t) cc_final: 0.6329 (p)
REVERT: D  316 GLN cc_start: 0.8162 (tt0) cc_final: 0.7875 (tt0)
REVERT: D  339 ASP cc_start: 0.6345 (m-30) cc_final: 0.6134 (m-30)
REVERT: B  100 MET cc_start: 0.7892 (mtt) cc_final: 0.7644 (mtt)
REVERT: B  173 ASN cc_start: 0.8116 (m-40) cc_final: 0.7732 (m-40)
REVERT: B  282 PHE cc_start: 0.7815 (t80) cc_final: 0.7546 (t80)
REVERT: C   34 ARG cc_start: 0.7432 (mtt90) cc_final: 0.7071 (mtm180)
REVERT: C   44 MET cc_start: 0.7084 (mmm) cc_final: 0.6594 (mmp)
REVERT: C  316 GLN cc_start: 0.8288 (tp40) cc_final: 0.7705 (tt0)
  outliers start: 19
  outliers final: 14
  residues processed: 246
  average time/residue: 0.2610
  time to fit residues: 96.2784
Evaluate side-chains
  242 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 225
  time to evaluate  : 1.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   63 GLU
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain D residue   19 GLN
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  272 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 128 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0060
   chunk 83 optimal weight:    1.9990
   chunk 137 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 138 optimal weight:    0.0980
   chunk 100 optimal weight:    2.9990
   chunk 123 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 139 optimal weight:    0.5980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 173 ASN
D 204 ASN
** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 204 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.166697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.148223 restraints weight = 37120.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 3.06
r_work: 0.3563 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14725  Z= 0.137
  Angle     :  0.586  13.365  19980  Z= 0.310
  Chirality :  0.041   0.211   2170
  Planarity :  0.004   0.042   2495
  Dihedral  :  3.967  17.389   1960
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.91 %
    Favored  : 81.97 %
  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:  1.35 (0.20), residues: 1710
  helix:  1.41 (0.14), residues: 1215
  sheet:  None (None), residues: 0
  loop : -0.25 (0.30), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  94 
 HIS   0.003   0.001   HIS D 156 
 PHE   0.053   0.002   PHE B  42 
 TYR   0.028   0.002   TYR B  85 
 ARG   0.011   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  975)
  hydrogen bonds       : angle       4.70501 ( 2815)
  covalent geometry    : bond        0.00288 (14725)
  covalent geometry    : angle       0.58592 (19980)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 236
  time to evaluate  : 1.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7291 (mtt90) cc_final: 0.6758 (mtm180)
REVERT: A   42 PHE cc_start: 0.7325 (m-80) cc_final: 0.6869 (m-80)
REVERT: A  202 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7694 (mtp180)
REVERT: A  203 ASP cc_start: 0.7276 (p0) cc_final: 0.6841 (m-30)
REVERT: A  249 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7182 (mp)
REVERT: E   44 MET cc_start: 0.6800 (mmm) cc_final: 0.6478 (mmm)
REVERT: E   63 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7526 (mp0)
REVERT: E  324 GLU cc_start: 0.8101 (tp30) cc_final: 0.7888 (tm-30)
REVERT: D   19 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6388 (mm110)
REVERT: D   32 LEU cc_start: 0.8230 (tp) cc_final: 0.7974 (tt)
REVERT: D   60 ARG cc_start: 0.6991 (mmp80) cc_final: 0.6761 (mmp80)
REVERT: D  149 LYS cc_start: 0.8223 (mttp) cc_final: 0.7921 (mttt)
REVERT: D  273 VAL cc_start: 0.6537 (t) cc_final: 0.6233 (p)
REVERT: D  316 GLN cc_start: 0.8132 (tt0) cc_final: 0.7920 (tt0)
REVERT: D  339 ASP cc_start: 0.6345 (m-30) cc_final: 0.6142 (m-30)
REVERT: B  173 ASN cc_start: 0.8125 (m-40) cc_final: 0.7748 (m-40)
REVERT: B  282 PHE cc_start: 0.7701 (t80) cc_final: 0.7498 (t80)
REVERT: C   34 ARG cc_start: 0.7461 (mtt90) cc_final: 0.7055 (mtm180)
REVERT: C   44 MET cc_start: 0.7074 (mmm) cc_final: 0.6623 (mmp)
REVERT: C  181 TYR cc_start: 0.8550 (p90) cc_final: 0.7702 (p90)
REVERT: C  316 GLN cc_start: 0.8304 (tp40) cc_final: 0.7723 (tt0)
  outliers start: 17
  outliers final: 13
  residues processed: 249
  average time/residue: 0.2750
  time to fit residues: 101.0349
Evaluate side-chains
  244 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 228
  time to evaluate  : 1.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   63 GLU
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain D residue   19 GLN
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  272 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 150 optimal weight:    0.8980
   chunk 97 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 144 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 142 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0670
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 173 ASN
** B 238 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 = 0.3898 r_free = 0.3898 target = 0.164136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.145575 restraints weight = 30927.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.97
r_work: 0.3563 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14725  Z= 0.147
  Angle     :  0.595  13.405  19980  Z= 0.313
  Chirality :  0.041   0.201   2170
  Planarity :  0.004   0.041   2495
  Dihedral  :  3.969  18.019   1960
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.17 %
    Favored  : 81.58 %
  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:  1.35 (0.20), residues: 1710
  helix:  1.40 (0.14), residues: 1215
  sheet:  None (None), residues: 0
  loop : -0.22 (0.30), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  94 
 HIS   0.003   0.001   HIS D 156 
 PHE   0.052   0.002   PHE B  42 
 TYR   0.030   0.002   TYR B  85 
 ARG   0.011   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04978 (  975)
  hydrogen bonds       : angle       4.71130 ( 2815)
  covalent geometry    : bond        0.00318 (14725)
  covalent geometry    : angle       0.59468 (19980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6489.09 seconds
wall clock time: 113 minutes 43.21 seconds (6823.21 seconds total)