Starting phenix.real_space_refine
on Thu Jul  2 05:21:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lqw_63307/07_2026/9lqw_63307.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lqw_63307/07_2026/9lqw_63307.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lqw_63307/07_2026/9lqw_63307.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lqw_63307/07_2026/9lqw_63307.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lqw_63307/07_2026/9lqw_63307.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lqw_63307/07_2026/9lqw_63307.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      60      5.16       5
     C    4566      2.51       5
     N    1000      2.21       5
     O    1142      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6770
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2157
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 11, 'TRANS': 259}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 954
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 954
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2157
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 11, 'TRANS': 259}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 954
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 954
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 274
          Unusual residues: {'CLR': 8, 'PCF': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
    Chain: "B"
      Number of atoms: 274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 274
          Unusual residues: {'CLR': 8, 'PCF': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
  Time building chain proxies: 1.68, per 1000 atoms: 0.25
  Number of scatterers: 6770
  At special positions: 0
  Unit cell: (99.51, 53.01, 107.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P       2     15.00
     O    1142      8.00
     N    1000      7.00
     C    4566      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 102 " - pdb=" SG  CYS A 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  33 " - pdb=" SG  CYS C 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 102 " - pdb=" SG  CYS B 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  33 " - pdb=" SG  CYS D 110 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 343.9 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1488

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 6 sheets defined
      58.0% alpha, 11.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 55
    Processing helix  chain 'A' and resid 64 through 80
    Processing helix  chain 'A' and resid 81 through 91
    Processing helix  chain 'A' and resid 98 through 132
    Processing helix  chain 'A' and resid 147 through 161
    Processing helix  chain 'A' and resid 161 through 167
    Processing helix  chain 'A' and resid 172 through 176
      removed outlier: 3.621A  pdb=" N   ASN A 175 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   THR A 176 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 172 through 176'
    Processing helix  chain 'A' and resid 193 through 229
      removed outlier: 3.558A  pdb=" N   TRP A 197 " --> pdb=" O   SER A 193 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   VAL A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      Proline residue:  A 213  - end of helix
    Processing helix  chain 'A' and resid 244 through 273
      removed outlier: 3.761A  pdb=" N   SER A 248 " --> pdb=" O   ARG A 244 " (cutoff:3.500A)
      Proline residue:  A 263  - end of helix
    Processing helix  chain 'A' and resid 280 through 301
      removed outlier: 3.556A  pdb=" N   PHE A 286 " --> pdb=" O   ASP A 282 " (cutoff:3.500A)
      Proline residue:  A 292  - end of helix
    Processing helix  chain 'A' and resid 304 through 313
    Processing helix  chain 'A' and resid 313 through 323
      removed outlier: 3.714A  pdb=" N   MET A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 90
    Processing helix  chain 'B' and resid 29 through 55
    Processing helix  chain 'B' and resid 64 through 80
    Processing helix  chain 'B' and resid 81 through 91
    Processing helix  chain 'B' and resid 98 through 132
    Processing helix  chain 'B' and resid 147 through 161
    Processing helix  chain 'B' and resid 161 through 167
    Processing helix  chain 'B' and resid 172 through 176
      removed outlier: 3.621A  pdb=" N   ASN B 175 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   THR B 176 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 172 through 176'
    Processing helix  chain 'B' and resid 193 through 229
      removed outlier: 3.561A  pdb=" N   TRP B 197 " --> pdb=" O   SER B 193 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   VAL B 212 " --> pdb=" O   VAL B 208 " (cutoff:3.500A)
      Proline residue:  B 213  - end of helix
    Processing helix  chain 'B' and resid 244 through 273
      removed outlier: 3.760A  pdb=" N   SER B 248 " --> pdb=" O   ARG B 244 " (cutoff:3.500A)
      Proline residue:  B 263  - end of helix
    Processing helix  chain 'B' and resid 280 through 301
      removed outlier: 3.556A  pdb=" N   PHE B 286 " --> pdb=" O   ASP B 282 " (cutoff:3.500A)
      Proline residue:  B 292  - end of helix
    Processing helix  chain 'B' and resid 304 through 313
    Processing helix  chain 'B' and resid 313 through 323
      removed outlier: 3.713A  pdb=" N   MET B 323 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171
    Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 7
      removed outlier: 4.042A  pdb=" N   LEU C  18 " --> pdb=" O   MET C  82 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   MET C  82 " --> pdb=" O   LEU C  18 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER C  70 " --> pdb=" O   TYR C  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 59
      removed outlier: 5.845A  pdb=" N   GLY C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ARG C  38 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   MET C  34 " --> pdb=" O   MET C  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171
    Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 7
      removed outlier: 4.168A  pdb=" N   LEU D  18 " --> pdb=" O   MET D  82 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   MET D  82 " --> pdb=" O   LEU D  18 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER D  70 " --> pdb=" O   TYR D  79 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 57 through 59
      removed outlier: 5.841A  pdb=" N   GLY D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ARG D  38 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   MET D  34 " --> pdb=" O   MET D  51 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1140 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: 0.84

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 934
        1.31 -     1.43: 1949
        1.43 -     1.56: 3879
        1.56 -     1.69: 122
        1.69 -     1.82: 92
  Bond restraints: 6976
  Sorted by residual:
  bond pdb=" N   PRO C  41 "
       pdb=" CD  PRO C  41 "
    ideal  model  delta    sigma   weight residual
    1.473  1.567 -0.094 1.40e-02 5.10e+03 4.50e+01
  bond pdb=" N   PRO D  41 "
       pdb=" CD  PRO D  41 "
    ideal  model  delta    sigma   weight residual
    1.473  1.567 -0.094 1.40e-02 5.10e+03 4.46e+01
  bond pdb=" C21 PCF B 401 "
       pdb=" O21 PCF B 401 "
    ideal  model  delta    sigma   weight residual
    1.334  1.435 -0.101 2.00e-02 2.50e+03 2.56e+01
  bond pdb=" C21 PCF A 401 "
       pdb=" O21 PCF A 401 "
    ideal  model  delta    sigma   weight residual
    1.334  1.435 -0.101 2.00e-02 2.50e+03 2.53e+01
  bond pdb=" C31 PCF B 401 "
       pdb=" O31 PCF B 401 "
    ideal  model  delta    sigma   weight residual
    1.329  1.419 -0.090 2.00e-02 2.50e+03 2.02e+01
  ... (remaining 6971 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.52: 9420
        4.52 -     9.04: 137
        9.04 -    13.56: 7
       13.56 -    18.08: 0
       18.08 -    22.61: 4
  Bond angle restraints: 9568
  Sorted by residual:
  angle pdb=" O12 PCF A 401 "
        pdb=" P   PCF A 401 "
        pdb=" O14 PCF A 401 "
      ideal   model   delta    sigma   weight residual
     123.69  101.08   22.61 3.00e+00 1.11e-01 5.68e+01
  angle pdb=" O12 PCF B 401 "
        pdb=" P   PCF B 401 "
        pdb=" O14 PCF B 401 "
      ideal   model   delta    sigma   weight residual
     123.69  101.15   22.54 3.00e+00 1.11e-01 5.65e+01
  angle pdb=" N   GLY D  42 "
        pdb=" CA  GLY D  42 "
        pdb=" C   GLY D  42 "
      ideal   model   delta    sigma   weight residual
     114.40  108.60    5.80 1.11e+00 8.12e-01 2.73e+01
  angle pdb=" N   GLY C  42 "
        pdb=" CA  GLY C  42 "
        pdb=" C   GLY C  42 "
      ideal   model   delta    sigma   weight residual
     114.40  108.65    5.75 1.11e+00 8.12e-01 2.68e+01
  angle pdb=" C   ALA C  40 "
        pdb=" N   PRO C  41 "
        pdb=" CD  PRO C  41 "
      ideal   model   delta    sigma   weight residual
     125.00  105.81   19.19 4.10e+00 5.95e-02 2.19e+01
  ... (remaining 9563 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.35: 4341
       22.35 -    44.71: 384
       44.71 -    67.06: 95
       67.06 -    89.41: 10
       89.41 -   111.77: 4
  Dihedral angle restraints: 4834
    sinusoidal: 2512
      harmonic: 2322
  Sorted by residual:
  dihedral pdb=" CB  CYS D  33 "
           pdb=" SG  CYS D  33 "
           pdb=" SG  CYS D 110 "
           pdb=" CB  CYS D 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -34.04  -51.96     1      1.00e+01 1.00e-02 3.68e+01
  dihedral pdb=" CB  CYS C  33 "
           pdb=" SG  CYS C  33 "
           pdb=" SG  CYS C 110 "
           pdb=" CB  CYS C 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -34.05  -51.95     1      1.00e+01 1.00e-02 3.68e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  95 "
           pdb=" CB  CYS D  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.58   32.42     1      1.00e+01 1.00e-02 1.50e+01
  ... (remaining 4831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 948
       0.069 -    0.139: 100
       0.139 -    0.208: 32
       0.208 -    0.278: 32
       0.278 -    0.347: 16
  Chirality restraints: 1128
  Sorted by residual:
  chirality pdb=" C17 CLR B 403 "
            pdb=" C13 CLR B 403 "
            pdb=" C16 CLR B 403 "
            pdb=" C20 CLR B 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.90   -0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" C17 CLR A 407 "
            pdb=" C13 CLR A 407 "
            pdb=" C16 CLR A 407 "
            pdb=" C20 CLR A 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.90   -0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" C17 CLR A 408 "
            pdb=" C13 CLR A 408 "
            pdb=" C16 CLR A 408 "
            pdb=" C20 CLR A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.89   -0.34 2.00e-01 2.50e+01 2.90e+00
  ... (remaining 1125 not shown)

  Planarity restraints: 1062
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D  40 "   -0.110 5.00e-02 4.00e+02   1.77e-01 5.00e+01
        pdb=" N   PRO D  41 "    0.306 5.00e-02 4.00e+02
        pdb=" CA  PRO D  41 "   -0.109 5.00e-02 4.00e+02
        pdb=" CD  PRO D  41 "   -0.087 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  40 "   -0.109 5.00e-02 4.00e+02   1.76e-01 4.96e+01
        pdb=" N   PRO C  41 "    0.305 5.00e-02 4.00e+02
        pdb=" CA  PRO C  41 "   -0.108 5.00e-02 4.00e+02
        pdb=" CD  PRO C  41 "   -0.087 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D  86 "    0.032 5.00e-02 4.00e+02   4.88e-02 3.82e+00
        pdb=" N   PRO D  87 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO D  87 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D  87 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1059 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1767
        2.81 -     3.33: 6221
        3.33 -     3.85: 11503
        3.85 -     4.38: 13147
        4.38 -     4.90: 23389
  Nonbonded interactions: 56027
  Sorted by model distance:
  nonbonded pdb=" O   SER C  27 "
            pdb=" ND2 ASN C  76 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   SER D  27 "
            pdb=" ND2 ASN D  76 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" NH2 ARG A  91 "
            pdb=" OD2 ASP A  94 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" NH2 ARG B  91 "
            pdb=" OD2 ASP B  94 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" OG1 THR D  19 "
            pdb=" OE1 GLN D  81 "
     model   vdw
     2.347 3.040
  ... (remaining 56022 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.080
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:5.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
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      :  0.009   0.101   6982  Z= 0.447
  Angle     :  1.236  22.606   9580  Z= 0.537
  Chirality :  0.075   0.347   1128
  Planarity :  0.009   0.177   1062
  Dihedral  : 16.788 111.767   3328
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 21.42
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  2.31 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 26.34 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.31), residues: 780
  helix:  1.74 (0.25), residues: 444
  sheet: -1.29 (0.56), residues: 98
  loop : -2.59 (0.33), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 245 
 TYR   0.011   0.001   TYR B  88 
 PHE   0.009   0.001   PHE A 291 
 TRP   0.008   0.001   TRP D  36 
 HIS   0.002   0.001   HIS D  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00862 /  0.45 ( 6976)
  covalent geometry    : angle       1.23616 /  0.54 ( 9568)
  SS BOND              : bond        0.00088 /  0.06 (    6)
  SS BOND              : angle       1.20194 /  0.76 (   12)
  hydrogen bonds       : bond        0.14376 /  9.65 (  388)
  hydrogen bonds       : angle       5.78988 /  4.37 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ARG cc_start: 0.5989 (ptm160) cc_final: 0.5181 (mtt90)
REVERT: B  244 ARG cc_start: 0.6047 (ptm160) cc_final: 0.5211 (mtt90)
  outliers start: 3
  outliers final: 2
  residues processed: 79
  average time/residue: 0.4428
  time to fit residues: 37.2085
Evaluate side-chains
  74 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain D residue  105 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  39 GLN
D  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.194042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.149361 restraints weight = 6695.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.44
r_work: 0.3274 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6982  Z= 0.137
  Angle     :  0.642   7.789   9580  Z= 0.300
  Chirality :  0.039   0.137   1128
  Planarity :  0.005   0.071   1062
  Dihedral  : 10.889  58.050   2018
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 21.58 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.31), residues: 780
  helix:  1.90 (0.25), residues: 446
  sheet: -0.26 (0.57), residues: 94
  loop : -2.69 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  91 
 TYR   0.010   0.001   TYR B  88 
 PHE   0.012   0.001   PHE B 291 
 TRP   0.006   0.001   TRP A  85 
 HIS   0.002   0.001   HIS D  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.14 ( 6976)
  covalent geometry    : angle       0.64171 /  0.30 ( 9568)
  SS BOND              : bond        0.00251 /  0.18 (    6)
  SS BOND              : angle       1.10033 /  0.72 (   12)
  hydrogen bonds       : bond        0.04708 /  3.12 (  388)
  hydrogen bonds       : angle       4.65627 /  3.50 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5905 (ptm160)
REVERT: B  244 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.5398 (mtt90)
  outliers start: 30
  outliers final: 13
  residues processed: 102
  average time/residue: 0.4149
  time to fit residues: 44.9360
Evaluate side-chains
  94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  244 ARG
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue   82 MET
Chi-restraints excluded: chain D residue   92 MET
Chi-restraints excluded: chain D residue  105 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    0.0270
   chunk 58 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.5640

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  39 GLN
D  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.189709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.139861 restraints weight = 6550.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.65
r_work: 0.3260 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6982  Z= 0.111
  Angle     :  0.578  10.416   9580  Z= 0.272
  Chirality :  0.037   0.122   1128
  Planarity :  0.004   0.041   1062
  Dihedral  : 10.026  58.103   2018
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 21.13 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.31), residues: 780
  helix:  2.05 (0.25), residues: 446
  sheet:  0.16 (0.57), residues: 92
  loop : -2.61 (0.33), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  91 
 TYR   0.008   0.001   TYR B 293 
 PHE   0.011   0.001   PHE A 291 
 TRP   0.006   0.001   TRP A  51 
 HIS   0.001   0.000   HIS C  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.11 ( 6976)
  covalent geometry    : angle       0.57754 /  0.27 ( 9568)
  SS BOND              : bond        0.00072 /  0.05 (    6)
  SS BOND              : angle       0.92473 /  0.57 (   12)
  hydrogen bonds       : bond        0.04298 /  2.83 (  388)
  hydrogen bonds       : angle       4.35695 /  3.26 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 75
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5515 (mtt90)
REVERT: B  244 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.5577 (mtt90)
  outliers start: 34
  outliers final: 12
  residues processed: 97
  average time/residue: 0.4136
  time to fit residues: 42.7738
Evaluate side-chains
  86 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  244 ARG
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue   92 MET
Chi-restraints excluded: chain D residue  105 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  39 GLN
D  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.187107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.142626 restraints weight = 6714.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.57
r_work: 0.3149 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   6982  Z= 0.250
  Angle     :  0.759  10.935   9580  Z= 0.357
  Chirality :  0.045   0.157   1128
  Planarity :  0.005   0.043   1062
  Dihedral  : 11.089  59.876   2018
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 21.13 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.30), residues: 780
  helix:  1.42 (0.24), residues: 446
  sheet: -0.61 (0.50), residues: 112
  loop : -2.55 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 100 
 TYR   0.016   0.002   TYR B  88 
 PHE   0.017   0.003   PHE A 214 
 TRP   0.011   0.002   TRP A  85 
 HIS   0.002   0.001   HIS C  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00587 /  0.25 ( 6976)
  covalent geometry    : angle       0.75839 /  0.36 ( 9568)
  SS BOND              : bond        0.00426 /  0.28 (    6)
  SS BOND              : angle       1.13509 /  0.72 (   12)
  hydrogen bonds       : bond        0.05911 /  4.01 (  388)
  hydrogen bonds       : angle       4.84433 /  3.63 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 79
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8173 (tpp) cc_final: 0.7972 (tpp)
REVERT: B  244 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.5473 (mtt90)
  outliers start: 36
  outliers final: 19
  residues processed: 98
  average time/residue: 0.4377
  time to fit residues: 45.8424
Evaluate side-chains
  101 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  114 MET
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  244 ARG
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  114 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0970
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.184525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.133845 restraints weight = 6679.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.23
r_work: 0.3205 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6982  Z= 0.135
  Angle     :  0.593   8.941   9580  Z= 0.285
  Chirality :  0.038   0.129   1128
  Planarity :  0.005   0.040   1062
  Dihedral  : 10.492  59.684   2018
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 22.62 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.30), residues: 780
  helix:  1.73 (0.25), residues: 446
  sheet:  0.21 (0.58), residues: 90
  loop : -2.56 (0.32), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  55 
 TYR   0.012   0.001   TYR A  88 
 PHE   0.011   0.001   PHE B 291 
 TRP   0.006   0.001   TRP A 261 
 HIS   0.001   0.000   HIS D  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 6976)
  covalent geometry    : angle       0.59248 /  0.28 ( 9568)
  SS BOND              : bond        0.00172 /  0.11 (    6)
  SS BOND              : angle       0.91639 /  0.58 (   12)
  hydrogen bonds       : bond        0.04749 /  3.17 (  388)
  hydrogen bonds       : angle       4.52996 /  3.40 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 75
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  244 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5576 (mtt90)
REVERT: B  192 SER cc_start: 0.7584 (OUTLIER) cc_final: 0.7281 (m)
REVERT: B  244 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5596 (mtt90)
  outliers start: 30
  outliers final: 18
  residues processed: 93
  average time/residue: 0.4133
  time to fit residues: 41.3174
Evaluate side-chains
  91 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 MET
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  244 ARG
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  105 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    0.9980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.185170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.134726 restraints weight = 6659.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.63
r_work: 0.3328 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6982  Z= 0.129
  Angle     :  0.581   8.725   9580  Z= 0.279
  Chirality :  0.038   0.127   1128
  Planarity :  0.004   0.039   1062
  Dihedral  : 10.212  58.241   2018
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 21.58 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.30), residues: 780
  helix:  1.84 (0.25), residues: 446
  sheet: -0.38 (0.51), residues: 110
  loop : -2.47 (0.34), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  55 
 TYR   0.010   0.001   TYR A  88 
 PHE   0.010   0.001   PHE B 291 
 TRP   0.006   0.001   TRP A 261 
 HIS   0.001   0.000   HIS C  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 6976)
  covalent geometry    : angle       0.58043 /  0.28 ( 9568)
  SS BOND              : bond        0.00210 /  0.14 (    6)
  SS BOND              : angle       0.88541 /  0.55 (   12)
  hydrogen bonds       : bond        0.04571 /  3.05 (  388)
  hydrogen bonds       : angle       4.45929 /  3.35 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  244 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5616 (mtt90)
REVERT: B  192 SER cc_start: 0.7528 (OUTLIER) cc_final: 0.7247 (m)
REVERT: B  244 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.5558 (mtt90)
  outliers start: 30
  outliers final: 17
  residues processed: 90
  average time/residue: 0.3633
  time to fit residues: 35.0119
Evaluate side-chains
  93 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 MET
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  244 ARG
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  114 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 30 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.7382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.191867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.148063 restraints weight = 6648.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.66
r_work: 0.3229 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6982  Z= 0.113
  Angle     :  0.551   8.362   9580  Z= 0.267
  Chirality :  0.037   0.121   1128
  Planarity :  0.004   0.039   1062
  Dihedral  :  9.832  58.277   2018
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.02 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.31), residues: 780
  helix:  1.97 (0.25), residues: 446
  sheet:  0.42 (0.58), residues: 90
  loop : -2.46 (0.32), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  53 
 TYR   0.008   0.001   TYR B 293 
 PHE   0.009   0.001   PHE B 291 
 TRP   0.005   0.001   TRP B 154 
 HIS   0.001   0.000   HIS D  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 ( 6976)
  covalent geometry    : angle       0.55016 /  0.27 ( 9568)
  SS BOND              : bond        0.00161 /  0.11 (    6)
  SS BOND              : angle       0.88582 /  0.55 (   12)
  hydrogen bonds       : bond        0.04333 /  2.88 (  388)
  hydrogen bonds       : angle       4.33642 /  3.26 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  244 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.5624 (mtt90)
REVERT: B  244 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5633 (mtt90)
  outliers start: 27
  outliers final: 19
  residues processed: 85
  average time/residue: 0.4377
  time to fit residues: 39.7384
Evaluate side-chains
  91 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  244 ARG
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   34 MET
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  114 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0370
   chunk 49 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.7462

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.186713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.135794 restraints weight = 6587.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.33
r_work: 0.3236 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6982  Z= 0.113
  Angle     :  0.549   8.316   9580  Z= 0.266
  Chirality :  0.037   0.145   1128
  Planarity :  0.004   0.039   1062
  Dihedral  :  9.725  59.080   2018
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 22.02 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.31), residues: 780
  helix:  2.01 (0.25), residues: 446
  sheet: -0.15 (0.51), residues: 110
  loop : -2.40 (0.34), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  55 
 TYR   0.008   0.001   TYR B 293 
 PHE   0.010   0.001   PHE A 291 
 TRP   0.005   0.001   TRP B 154 
 HIS   0.001   0.000   HIS C  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 ( 6976)
  covalent geometry    : angle       0.54893 /  0.27 ( 9568)
  SS BOND              : bond        0.00122 /  0.08 (    6)
  SS BOND              : angle       0.84765 /  0.53 (   12)
  hydrogen bonds       : bond        0.04310 /  2.86 (  388)
  hydrogen bonds       : angle       4.30359 /  3.23 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  244 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5665 (mtt90)
REVERT: B  244 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.5654 (mtt90)
  outliers start: 26
  outliers final: 18
  residues processed: 87
  average time/residue: 0.4328
  time to fit residues: 39.8523
Evaluate side-chains
  91 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  244 ARG
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  114 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0970
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0770
   chunk 13 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.8140

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.192282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.148090 restraints weight = 6729.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.74
r_work: 0.3307 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6982  Z= 0.115
  Angle     :  0.549   8.262   9580  Z= 0.266
  Chirality :  0.037   0.123   1128
  Planarity :  0.004   0.039   1062
  Dihedral  :  9.724  59.742   2018
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.62 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.30), residues: 780
  helix:  2.02 (0.25), residues: 446
  sheet: -0.12 (0.51), residues: 110
  loop : -2.37 (0.34), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 100 
 TYR   0.009   0.001   TYR A 293 
 PHE   0.009   0.001   PHE B 291 
 TRP   0.005   0.001   TRP A 261 
 HIS   0.001   0.000   HIS D  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 ( 6976)
  covalent geometry    : angle       0.54825 /  0.27 ( 9568)
  SS BOND              : bond        0.00117 /  0.08 (    6)
  SS BOND              : angle       0.82941 /  0.52 (   12)
  hydrogen bonds       : bond        0.04341 /  2.89 (  388)
  hydrogen bonds       : angle       4.30294 /  3.24 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  244 ARG cc_start: 0.6374 (OUTLIER) cc_final: 0.5696 (mtt90)
REVERT: B  244 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.5708 (mtt90)
  outliers start: 21
  outliers final: 19
  residues processed: 82
  average time/residue: 0.4414
  time to fit residues: 38.6483
Evaluate side-chains
  92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  244 ARG
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   34 MET
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  114 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 66 optimal weight:   20.0000
   chunk 5 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0870
   chunk 40 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 72 optimal weight:    9.9990
   overall best weight:    0.6760

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.188729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.143643 restraints weight = 6694.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.52
r_work: 0.3317 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6982  Z= 0.109
  Angle     :  0.539   8.159   9580  Z= 0.262
  Chirality :  0.037   0.153   1128
  Planarity :  0.004   0.039   1062
  Dihedral  :  9.647  59.777   2018
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 22.02 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.31), residues: 780
  helix:  2.07 (0.25), residues: 446
  sheet: -0.02 (0.51), residues: 110
  loop : -2.39 (0.34), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 100 
 TYR   0.008   0.001   TYR B 293 
 PHE   0.010   0.001   PHE A 291 
 TRP   0.005   0.001   TRP B 154 
 HIS   0.001   0.000   HIS C  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 6976)
  covalent geometry    : angle       0.53849 /  0.26 ( 9568)
  SS BOND              : bond        0.00100 /  0.07 (    6)
  SS BOND              : angle       0.82782 /  0.52 (   12)
  hydrogen bonds       : bond        0.04251 /  2.83 (  388)
  hydrogen bonds       : angle       4.24244 /  3.19 ( 1140)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  244 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.5696 (mtt90)
REVERT: B  244 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5693 (mtt90)
  outliers start: 26
  outliers final: 19
  residues processed: 88
  average time/residue: 0.4215
  time to fit residues: 39.6426
Evaluate side-chains
  92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  244 ARG
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   34 MET
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  114 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0020
   chunk 23 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0270
   chunk 4 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 27 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.5246

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.193437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.149011 restraints weight = 6683.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.39
r_work: 0.3340 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6982  Z= 0.105
  Angle     :  0.539   8.056   9580  Z= 0.261
  Chirality :  0.036   0.132   1128
  Planarity :  0.004   0.039   1062
  Dihedral  :  9.499  59.521   2018
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.62 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.30), residues: 780
  helix:  2.14 (0.25), residues: 446
  sheet:  0.69 (0.57), residues: 90
  loop : -2.41 (0.32), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.008   0.001   TYR B 293 
 PHE   0.010   0.001   PHE B 291 
 TRP   0.005   0.001   TRP B 154 
 HIS   0.001   0.000   HIS C  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00224 /  0.10 ( 6976)
  covalent geometry    : angle       0.53833 /  0.26 ( 9568)
  SS BOND              : bond        0.00071 /  0.05 (    6)
  SS BOND              : angle       0.81224 /  0.50 (   12)
  hydrogen bonds       : bond        0.04107 /  2.72 (  388)
  hydrogen bonds       : angle       4.19832 /  3.17 ( 1140)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2137.50 seconds
wall clock time: 37 minutes 15.69 seconds (2235.69 seconds total)