Starting phenix.real_space_refine
on Sat May 10 04:02:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cb3_45413/05_2025/9cb3_45413.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cb3_45413/05_2025/9cb3_45413.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cb3_45413/05_2025/9cb3_45413.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cb3_45413/05_2025/9cb3_45413.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cb3_45413/05_2025/9cb3_45413.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cb3_45413/05_2025/9cb3_45413.cif"
  }
  resolution = 3.47
  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=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3183      2.51       5
     N     882      2.21       5
     O     902      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4995
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 519, 3912
          Classifications: {'peptide': 519}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 504}
          Unresolved non-hydrogen bonds: 223
          Unresolved non-hydrogen angles: 278
          Unresolved non-hydrogen dihedrals: 178
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 153
    Chain: "B"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 967
          Classifications: {'peptide': 140}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PTRANS': 5, 'TRANS': 134}
          Chain breaks: 3
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 168
          Unresolved non-hydrogen angles: 211
          Unresolved non-hydrogen dihedrals: 140
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 90
    Chain: "C"
      Number of atoms: 116
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 13, 105
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 13, 105
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 94
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG C  85 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C  85 " occ=0.50
  Time building chain proxies: 3.75, per 1000 atoms: 0.75
  Number of scatterers: 4995
  At special positions: 0
  Unit cell: (77.655, 83.5, 97.695, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     902      8.00
     N     882      7.00
     C    3183      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: 1.31
  Conformation dependent library (CDL) restraints added in 666.2 milliseconds
  

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1296

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      72.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 35
      removed outlier: 3.617A  pdb=" N   LEU A  35 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 44
    Processing helix  chain 'A' and resid 45 through 47
      No H-bonds generated for 'chain 'A' and resid 45 through 47'
    Processing helix  chain 'A' and resid 48 through 56
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 70 through 75
    Processing helix  chain 'A' and resid 84 through 86
      No H-bonds generated for 'chain 'A' and resid 84 through 86'
    Processing helix  chain 'A' and resid 87 through 97
      removed outlier: 3.684A  pdb=" N   PHE A  91 " --> pdb=" O   ASN A  87 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A  97 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 113
      removed outlier: 3.929A  pdb=" N   ALA A 103 " --> pdb=" O   ASN A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 141
      removed outlier: 3.988A  pdb=" N   VAL A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 153
      removed outlier: 3.671A  pdb=" N   PHE A 152 " --> pdb=" O   ILE A 149 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE A 153 " --> pdb=" O   TRP A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 179
    Processing helix  chain 'A' and resid 183 through 196
      removed outlier: 4.088A  pdb=" N   LEU A 196 " --> pdb=" O   ARG A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 217
      removed outlier: 3.510A  pdb=" N   GLU A 212 " --> pdb=" O   ASP A 208 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 231
      removed outlier: 3.725A  pdb=" N   ARG A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 254
      removed outlier: 3.668A  pdb=" N   LYS A 253 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLY A 254 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 266
      removed outlier: 3.647A  pdb=" N   LYS A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 296 through 302
      removed outlier: 3.644A  pdb=" N   GLN A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 324
    Processing helix  chain 'A' and resid 327 through 345
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'A' and resid 351 through 367
    Processing helix  chain 'A' and resid 373 through 380
      removed outlier: 3.545A  pdb=" N   TRP A 379 " --> pdb=" O   ARG A 375 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 380 " --> pdb=" O   GLU A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 401
    Processing helix  chain 'A' and resid 409 through 419
      removed outlier: 3.851A  pdb=" N   TYR A 413 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 437
    Processing helix  chain 'A' and resid 442 through 447
      removed outlier: 3.630A  pdb=" N   TYR A 447 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 464
      removed outlier: 3.612A  pdb=" N   HIS A 464 " --> pdb=" O   ALA A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 479
    Processing helix  chain 'A' and resid 485 through 498
    Processing helix  chain 'A' and resid 511 through 517
    Processing helix  chain 'A' and resid 518 through 523
      removed outlier: 6.235A  pdb=" N   ARG A 521 " --> pdb=" O   GLU A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 528
      removed outlier: 3.789A  pdb=" N   GLN A 527 " --> pdb=" O   GLU A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 541
    Processing helix  chain 'B' and resid 17 through 22
    Processing helix  chain 'B' and resid 24 through 35
      removed outlier: 3.954A  pdb=" N   LYS B  28 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 65
    Processing helix  chain 'B' and resid 86 through 93
    Processing helix  chain 'B' and resid 96 through 111
    Processing helix  chain 'B' and resid 116 through 129
      removed outlier: 3.778A  pdb=" N   MET B 126 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   GLY B 129 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 139
    Processing helix  chain 'B' and resid 146 through 148
      No H-bonds generated for 'chain 'B' and resid 146 through 148'
    Processing helix  chain 'B' and resid 149 through 157

    293 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        1.18 -     1.41: 2036
        1.41 -     1.64: 3012
        1.64 -     1.87: 36
        1.87 -     2.10: 0
        2.10 -     2.33: 1
  Bond restraints: 5085
  Sorted by residual:
  bond pdb=" C   GLY C  84 "
       pdb=" N  AARG C  85 "
    ideal  model  delta    sigma   weight residual
    1.331  2.335 -1.004 2.07e-02 2.33e+03 2.35e+03
  bond pdb=" C   GLY C  84 "
       pdb=" N  BARG C  85 "
    ideal  model  delta    sigma   weight residual
    1.331  1.175  0.156 2.07e-02 2.33e+03 5.67e+01
  bond pdb=" C   SER A  77 "
       pdb=" O   SER A  77 "
    ideal  model  delta    sigma   weight residual
    1.234  1.180  0.054 1.35e-02 5.49e+03 1.61e+01
  bond pdb=" CA  ALA A  76 "
       pdb=" CB  ALA A  76 "
    ideal  model  delta    sigma   weight residual
    1.530  1.471  0.059 1.58e-02 4.01e+03 1.39e+01
  bond pdb=" C   SER A  77 "
       pdb=" N   PHE A  78 "
    ideal  model  delta    sigma   weight residual
    1.329  1.287  0.042 1.23e-02 6.61e+03 1.17e+01
  ... (remaining 5080 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.23: 6918
       14.23 -    28.45: 1
       28.45 -    42.68: 4
       42.68 -    56.90: 1
       56.90 -    71.13: 1
  Bond angle restraints: 6925
  Sorted by residual:
  angle pdb=" O   GLY C  84 "
        pdb=" C   GLY C  84 "
        pdb=" N  AARG C  85 "
      ideal   model   delta    sigma   weight residual
     123.00   72.01   50.99 1.60e+00 3.91e-01 1.02e+03
  angle pdb=" C   GLY C  84 "
        pdb=" N  AARG C  85 "
        pdb=" CA AARG C  85 "
      ideal   model   delta    sigma   weight residual
     121.80   50.67   71.13 2.44e+00 1.68e-01 8.50e+02
  angle pdb=" O   GLY C  84 "
        pdb=" C   GLY C  84 "
        pdb=" N  BARG C  85 "
      ideal   model   delta    sigma   weight residual
     123.00  162.27  -39.27 1.60e+00 3.91e-01 6.02e+02
  angle pdb=" CA  GLY C  84 "
        pdb=" C   GLY C  84 "
        pdb=" N  BARG C  85 "
      ideal   model   delta    sigma   weight residual
     116.20   78.13   38.07 2.00e+00 2.50e-01 3.62e+02
  angle pdb=" CA  GLY C  84 "
        pdb=" C   GLY C  84 "
        pdb=" N  AARG C  85 "
      ideal   model   delta    sigma   weight residual
     116.20  153.14  -36.94 2.00e+00 2.50e-01 3.41e+02
  ... (remaining 6920 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.98: 2927
       35.98 -    71.97: 117
       71.97 -   107.95: 6
      107.95 -   143.93: 1
      143.93 -   179.91: 1
  Dihedral angle restraints: 3052
    sinusoidal: 1073
      harmonic: 1979
  Sorted by residual:
  dihedral pdb=" CA  GLY C  84 "
           pdb=" C   GLY C  84 "
           pdb=" N  AARG C  85 "
           pdb=" CA AARG C  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   71.66  108.34     0      5.00e+00 4.00e-02 4.70e+02
  dihedral pdb=" CD BARG C  85 "
           pdb=" NE BARG C  85 "
           pdb=" CZ BARG C  85 "
           pdb=" NH1BARG C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  179.91 -179.91     1      1.00e+01 1.00e-02 1.92e+02
  dihedral pdb=" C   ASN B 108 "
           pdb=" N   ASN B 108 "
           pdb=" CA  ASN B 108 "
           pdb=" CB  ASN B 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.00  -12.60     0      2.50e+00 1.60e-01 2.54e+01
  ... (remaining 3049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 758
       0.068 -    0.136: 61
       0.136 -    0.205: 6
       0.205 -    0.273: 4
       0.273 -    0.341: 1
  Chirality restraints: 830
  Sorted by residual:
  chirality pdb=" CA  ASN B 108 "
            pdb=" N   ASN B 108 "
            pdb=" C   ASN B 108 "
            pdb=" CB  ASN B 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" CA  ILE B 112 "
            pdb=" N   ILE B 112 "
            pdb=" C   ILE B 112 "
            pdb=" CB  ILE B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CG  LEU A 434 "
            pdb=" CB  LEU A 434 "
            pdb=" CD1 LEU A 434 "
            pdb=" CD2 LEU A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 827 not shown)

  Planarity restraints: 879
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  84 "   -0.127 2.00e-02 2.50e+03   1.43e-01 2.05e+02
        pdb=" C   GLY C  84 "    0.242 2.00e-02 2.50e+03
        pdb=" O   GLY C  84 "   -0.044 2.00e-02 2.50e+03
        pdb=" N  AARG C  85 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 102 "    0.025 2.00e-02 2.50e+03   4.93e-02 2.43e+01
        pdb=" C   GLU B 102 "   -0.085 2.00e-02 2.50e+03
        pdb=" O   GLU B 102 "    0.032 2.00e-02 2.50e+03
        pdb=" N   LEU B 103 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  84 "   -0.006 2.00e-02 2.50e+03   3.73e-02 1.39e+01
        pdb=" C   GLY C  84 "    0.063 2.00e-02 2.50e+03
        pdb=" O   GLY C  84 "   -0.029 2.00e-02 2.50e+03
        pdb=" N  BARG C  85 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 876 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     2.01: 2
        2.01 -     2.74: 414
        2.74 -     3.46: 7399
        3.46 -     4.18: 10668
        4.18 -     4.90: 19337
  Nonbonded interactions: 37820
  Sorted by model distance:
  nonbonded pdb=" C   GLY C  84 "
            pdb=" CB AARG C  85 "
     model   vdw
     1.293 2.936
  nonbonded pdb=" N   GLY C  84 "
            pdb=" N  BARG C  85 "
     model   vdw
     1.931 2.560
  nonbonded pdb=" O   GLY C  84 "
            pdb=" CB AARG C  85 "
     model   vdw
     2.196 3.440
  nonbonded pdb=" OG  SER A 158 "
            pdb=" O   SER A 160 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   TYR A 350 "
            pdb=" OH  TYR A 385 "
     model   vdw
     2.244 3.040
  ... (remaining 37815 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:                  0.000
  Normalize map: mean=0, sd=1:             1.200
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.050
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
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      :  0.015   1.004   5085  Z= 0.741
  Angle     :  1.615  71.125   6925  Z= 0.857
  Chirality :  0.046   0.341    830
  Planarity :  0.007   0.143    879
  Dihedral  : 18.757 179.913   1756
  Min Nonbonded Distance : 1.293

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 33.33 %
    Favored  : 65.21 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.03 (0.34), residues: 661
  helix:  0.65 (0.26), residues: 451
  sheet:  None (None), residues: 0
  loop : -1.27 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  73 
 HIS   0.004   0.001   HIS A  69 
 PHE   0.025   0.002   PHE A 210 
 TYR   0.017   0.002   TYR A 223 
 ARG   0.004   0.000   ARG A 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15545 (  293)
  hydrogen bonds       : angle       6.01486 (  858)
  covalent geometry    : bond        0.01490 ( 5085)
  covalent geometry    : angle       1.61499 ( 6925)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 81
  average time/residue: 0.1711
  time to fit residues: 18.2410
Evaluate side-chains
  75 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain B residue  153 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0470
   chunk 51 optimal weight:    9.9990
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0770
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.219653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.159670 restraints weight = 6642.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 3.73
r_work: 0.3789 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3795
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3795 r_free = 0.3795    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3794 r_free = 0.3794    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3794
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.1016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5085  Z= 0.128
  Angle     :  0.627  13.564   6925  Z= 0.320
  Chirality :  0.039   0.276    830
  Planarity :  0.005   0.055    879
  Dihedral  :  8.309 178.895    719
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.09 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 29.17 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.15 %

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:  0.52 (0.34), residues: 662
  helix:  1.02 (0.26), residues: 457
  sheet:  None (None), residues: 0
  loop : -1.12 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  82 
 HIS   0.003   0.001   HIS A  69 
 PHE   0.014   0.001   PHE B 101 
 TYR   0.018   0.002   TYR A 341 
 ARG   0.002   0.000   ARG A 521 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04016 (  293)
  hydrogen bonds       : angle       4.25843 (  858)
  covalent geometry    : bond        0.00269 ( 5085)
  covalent geometry    : angle       0.62654 ( 6925)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 SER cc_start: 0.8072 (t) cc_final: 0.7571 (t)
REVERT: A  452 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7258 (tt)
REVERT: A  486 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.6201 (mp)
  outliers start: 24
  outliers final: 12
  residues processed: 102
  average time/residue: 0.1550
  time to fit residues: 21.0025
Evaluate side-chains
  86 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain B residue  126 MET
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  153 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0000
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.223856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.162961 restraints weight = 6449.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 3.80
r_work: 0.3789 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3792 r_free = 0.3792    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3792 r_free = 0.3792    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6608
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5085  Z= 0.121
  Angle     :  0.584  10.817   6925  Z= 0.292
  Chirality :  0.040   0.271    830
  Planarity :  0.005   0.050    879
  Dihedral  :  8.105 179.936    718
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 28.96 %
    Favored  : 66.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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:  0.81 (0.35), residues: 662
  helix:  1.24 (0.26), residues: 454
  sheet:  None (None), residues: 0
  loop : -0.97 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  73 
 HIS   0.003   0.001   HIS A  69 
 PHE   0.011   0.001   PHE B 101 
 TYR   0.021   0.002   TYR A 341 
 ARG   0.005   0.000   ARG A 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03559 (  293)
  hydrogen bonds       : angle       4.00132 (  858)
  covalent geometry    : bond        0.00269 ( 5085)
  covalent geometry    : angle       0.58373 ( 6925)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LEU cc_start: 0.7210 (tp) cc_final: 0.6794 (mt)
REVERT: A  452 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7141 (tt)
REVERT: A  486 ILE cc_start: 0.6477 (OUTLIER) cc_final: 0.6159 (mp)
REVERT: A  519 ASP cc_start: 0.8591 (t70) cc_final: 0.8112 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 95
  average time/residue: 0.1588
  time to fit residues: 20.0148
Evaluate side-chains
  89 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  521 ARG
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain B residue  126 MET
Chi-restraints excluded: chain B residue  153 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 27 optimal weight:   30.0000
   chunk 5 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0570
   overall best weight:    0.6700

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

Flipped N/Q/H residues before XYZ refinement:
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.219501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.151336 restraints weight = 12784.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 5.47
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3880 r_free = 0.3880    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3880 r_free = 0.3880    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6632
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5085  Z= 0.115
  Angle     :  0.561  12.187   6925  Z= 0.279
  Chirality :  0.038   0.206    830
  Planarity :  0.004   0.046    879
  Dihedral  :  7.963 178.793    718
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 29.58 %
    Favored  : 64.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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:  0.97 (0.35), residues: 662
  helix:  1.37 (0.26), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.92 (0.45), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  73 
 HIS   0.002   0.001   HIS B  65 
 PHE   0.009   0.001   PHE A 433 
 TYR   0.022   0.002   TYR A 341 
 ARG   0.005   0.000   ARG A 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03367 (  293)
  hydrogen bonds       : angle       3.94146 (  858)
  covalent geometry    : bond        0.00259 ( 5085)
  covalent geometry    : angle       0.56133 ( 6925)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LEU cc_start: 0.7177 (tp) cc_final: 0.6777 (mt)
REVERT: A  204 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7950 (pp30)
REVERT: A  255 CYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6574 (t)
REVERT: A  452 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7088 (tt)
REVERT: A  486 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6548 (mp)
  outliers start: 26
  outliers final: 17
  residues processed: 96
  average time/residue: 0.1588
  time to fit residues: 19.8591
Evaluate side-chains
  97 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  204 GLN
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  521 ARG
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain B residue  126 MET
Chi-restraints excluded: chain B residue  153 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.221705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.160644 restraints weight = 6426.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 3.78
r_work: 0.3763 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3764
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3764 r_free = 0.3764    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3764 r_free = 0.3764    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3764
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5085  Z= 0.123
  Angle     :  0.567  12.122   6925  Z= 0.279
  Chirality :  0.038   0.187    830
  Planarity :  0.004   0.045    879
  Dihedral  :  7.911 179.730    718
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 29.38 %
    Favored  : 64.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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:  1.04 (0.35), residues: 662
  helix:  1.40 (0.26), residues: 454
  sheet:  None (None), residues: 0
  loop : -0.84 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 226 
 HIS   0.003   0.001   HIS A  69 
 PHE   0.012   0.001   PHE A 497 
 TYR   0.027   0.002   TYR A 341 
 ARG   0.006   0.000   ARG A 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03438 (  293)
  hydrogen bonds       : angle       3.94780 (  858)
  covalent geometry    : bond        0.00285 ( 5085)
  covalent geometry    : angle       0.56660 ( 6925)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 78
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6932 (mmm-85)
REVERT: A   67 ASP cc_start: 0.6824 (m-30) cc_final: 0.6207 (m-30)
REVERT: A  129 LEU cc_start: 0.7245 (tp) cc_final: 0.6825 (mt)
REVERT: A  452 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7285 (tt)
REVERT: A  486 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6367 (mp)
REVERT: A  519 ASP cc_start: 0.8657 (t70) cc_final: 0.8171 (t0)
REVERT: A  521 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6987 (tmm160)
REVERT: B  155 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5096 (ptmt)
  outliers start: 29
  outliers final: 20
  residues processed: 97
  average time/residue: 0.1651
  time to fit residues: 21.0001
Evaluate side-chains
  97 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   56 ARG
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  521 ARG
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain B residue  126 MET
Chi-restraints excluded: chain B residue  155 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.220484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.157801 restraints weight = 7302.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 4.07
r_work: 0.3728 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3730 r_free = 0.3730    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3730 r_free = 0.3730    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5085  Z= 0.132
  Angle     :  0.584  12.863   6925  Z= 0.289
  Chirality :  0.039   0.194    830
  Planarity :  0.004   0.045    879
  Dihedral  :  7.646 177.933    717
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  6.46 %
    Allowed  : 28.75 %
    Favored  : 64.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.11 (0.35), residues: 662
  helix:  1.44 (0.26), residues: 454
  sheet:  None (None), residues: 0
  loop : -0.79 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 226 
 HIS   0.002   0.001   HIS A  69 
 PHE   0.012   0.001   PHE A 433 
 TYR   0.025   0.002   TYR A 341 
 ARG   0.005   0.000   ARG A 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  293)
  hydrogen bonds       : angle       3.95008 (  858)
  covalent geometry    : bond        0.00314 ( 5085)
  covalent geometry    : angle       0.58355 ( 6925)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7053 (tmm-80)
REVERT: A  129 LEU cc_start: 0.7283 (tp) cc_final: 0.6849 (mt)
REVERT: A  255 CYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6330 (t)
REVERT: A  287 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.5864 (t80)
REVERT: A  452 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7285 (tt)
REVERT: A  486 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6349 (mp)
REVERT: B  126 MET cc_start: 0.7836 (mmt) cc_final: 0.7539 (mtt)
REVERT: B  155 LYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5259 (tptt)
  outliers start: 30
  outliers final: 22
  residues processed: 99
  average time/residue: 0.1590
  time to fit residues: 20.3607
Evaluate side-chains
  107 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   56 ARG
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  155 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0470
   chunk 24 optimal weight:    0.0270
   chunk 53 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0980
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
A 216 GLN
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 464 HIS ** 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 = 0.4534 r_free = 0.4534 target = 0.224179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.162847 restraints weight = 6845.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 3.93
r_work: 0.3780 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6642
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5085  Z= 0.100
  Angle     :  0.569  12.616   6925  Z= 0.276
  Chirality :  0.039   0.227    830
  Planarity :  0.004   0.046    879
  Dihedral  :  7.607 178.801    717
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 30.42 %
    Favored  : 64.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.29 (0.35), residues: 662
  helix:  1.53 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -0.59 (0.47), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 226 
 HIS   0.003   0.001   HIS A  69 
 PHE   0.006   0.001   PHE A 134 
 TYR   0.026   0.002   TYR A 223 
 ARG   0.005   0.000   ARG A 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03049 (  293)
  hydrogen bonds       : angle       3.88971 (  858)
  covalent geometry    : bond        0.00220 ( 5085)
  covalent geometry    : angle       0.56873 ( 6925)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6899 (tmm-80)
REVERT: A  129 LEU cc_start: 0.7346 (tp) cc_final: 0.6911 (mt)
REVERT: A  452 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7079 (tt)
REVERT: A  486 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6304 (mp)
REVERT: A  519 ASP cc_start: 0.8598 (t70) cc_final: 0.8206 (t0)
REVERT: B  126 MET cc_start: 0.7800 (mmt) cc_final: 0.7513 (mtt)
REVERT: B  155 LYS cc_start: 0.6169 (OUTLIER) cc_final: 0.4907 (ptmt)
REVERT: B  156 GLU cc_start: 0.4046 (mm-30) cc_final: 0.3681 (pt0)
  outliers start: 22
  outliers final: 17
  residues processed: 98
  average time/residue: 0.1656
  time to fit residues: 20.9001
Evaluate side-chains
  93 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ARG
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain B residue  155 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.222821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.161333 restraints weight = 6758.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 3.89
r_work: 0.3743 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3727 r_free = 0.3727    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3727 r_free = 0.3727    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5085  Z= 0.132
  Angle     :  0.585  12.777   6925  Z= 0.287
  Chirality :  0.039   0.190    830
  Planarity :  0.004   0.045    879
  Dihedral  :  7.620 178.385    717
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 29.58 %
    Favored  : 64.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.21 (0.35), residues: 662
  helix:  1.48 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -0.65 (0.47), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 226 
 HIS   0.003   0.001   HIS A 215 
 PHE   0.012   0.001   PHE A 433 
 TYR   0.027   0.002   TYR A 223 
 ARG   0.007   0.000   ARG A 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  293)
  hydrogen bonds       : angle       3.94367 (  858)
  covalent geometry    : bond        0.00307 ( 5085)
  covalent geometry    : angle       0.58503 ( 6925)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 75
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6858 (tt0)
REVERT: A  129 LEU cc_start: 0.7328 (tp) cc_final: 0.6903 (mt)
REVERT: A  287 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.5863 (t80)
REVERT: A  452 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7277 (tt)
REVERT: A  486 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6378 (mp)
REVERT: A  524 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7896 (mt-10)
REVERT: B  126 MET cc_start: 0.7794 (mmt) cc_final: 0.7547 (mtt)
REVERT: B  155 LYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5358 (tptt)
  outliers start: 28
  outliers final: 20
  residues processed: 93
  average time/residue: 0.1707
  time to fit residues: 20.5411
Evaluate side-chains
  100 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ARG
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  521 ARG
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  155 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 45 optimal weight:    0.0870
   chunk 23 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    0.1980
   chunk 55 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.6162

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.224794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.173137 restraints weight = 7096.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 3.90
r_work: 0.3789 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3789 r_free = 0.3789    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3789 r_free = 0.3789    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6587
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5085  Z= 0.114
  Angle     :  0.602  13.052   6925  Z= 0.295
  Chirality :  0.039   0.193    830
  Planarity :  0.004   0.046    879
  Dihedral  :  7.621 178.746    717
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 30.42 %
    Favored  : 63.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.31 (0.35), residues: 662
  helix:  1.52 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -0.54 (0.47), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  73 
 HIS   0.002   0.001   HIS B  65 
 PHE   0.008   0.001   PHE A 100 
 TYR   0.038   0.002   TYR A 223 
 ARG   0.007   0.000   ARG A 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03226 (  293)
  hydrogen bonds       : angle       3.87749 (  858)
  covalent geometry    : bond        0.00257 ( 5085)
  covalent geometry    : angle       0.60195 ( 6925)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6980 (tmm-80)
REVERT: A  129 LEU cc_start: 0.7302 (tp) cc_final: 0.6861 (mt)
REVERT: A  287 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.5737 (t80)
REVERT: A  452 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7163 (tt)
REVERT: A  486 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.6238 (mp)
REVERT: B  126 MET cc_start: 0.7772 (mmt) cc_final: 0.7523 (mtt)
REVERT: B  155 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5343 (ptmt)
  outliers start: 26
  outliers final: 18
  residues processed: 93
  average time/residue: 0.1934
  time to fit residues: 22.8779
Evaluate side-chains
  95 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ARG
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  521 ARG
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  155 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    8.9990
   chunk 51 optimal weight:   20.0000
   chunk 45 optimal weight:    0.0770
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    0.3980
   chunk 19 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** A 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.225560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.160710 restraints weight = 9714.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 4.77
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5085  Z= 0.112
  Angle     :  0.602  12.942   6925  Z= 0.294
  Chirality :  0.039   0.200    830
  Planarity :  0.004   0.046    879
  Dihedral  :  7.633 179.217    717
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 30.62 %
    Favored  : 64.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 (0.35), residues: 662
  helix:  1.50 (0.26), residues: 456
  sheet:  None (None), residues: 0
  loop : -0.37 (0.47), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 226 
 HIS   0.002   0.000   HIS A  69 
 PHE   0.007   0.001   PHE A 100 
 TYR   0.035   0.002   TYR A 223 
 ARG   0.009   0.001   ARG A 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03142 (  293)
  hydrogen bonds       : angle       3.84281 (  858)
  covalent geometry    : bond        0.00248 ( 5085)
  covalent geometry    : angle       0.60155 ( 6925)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LEU cc_start: 0.7222 (tp) cc_final: 0.6804 (mt)
REVERT: A  287 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.5585 (t80)
REVERT: A  452 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7034 (tt)
REVERT: A  486 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6540 (mp)
REVERT: B  126 MET cc_start: 0.7668 (mmt) cc_final: 0.7381 (mtm)
REVERT: B  155 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.5480 (ptmt)
  outliers start: 21
  outliers final: 17
  residues processed: 88
  average time/residue: 0.1771
  time to fit residues: 20.3843
Evaluate side-chains
  90 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ARG
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  521 ARG
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue  155 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0270
   chunk 30 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6438

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.225129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.172976 restraints weight = 10489.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.4041 rms_B_bonded: 6.43
r_work: 0.3679 rms_B_bonded: 6.08 restraints_weight: 2.0000
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3667
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3667 r_free = 0.3667    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3667 r_free = 0.3667    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3667
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5085  Z= 0.117
  Angle     :  0.611  13.073   6925  Z= 0.297
  Chirality :  0.040   0.296    830
  Planarity :  0.004   0.046    879
  Dihedral  :  7.630 178.800    717
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 29.79 %
    Favored  : 65.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.26 (0.35), residues: 662
  helix:  1.44 (0.26), residues: 457
  sheet:  None (None), residues: 0
  loop : -0.46 (0.47), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 226 
 HIS   0.002   0.001   HIS A 429 
 PHE   0.008   0.001   PHE A 100 
 TYR   0.037   0.002   TYR A 223 
 ARG   0.009   0.000   ARG A 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03185 (  293)
  hydrogen bonds       : angle       3.84933 (  858)
  covalent geometry    : bond        0.00266 ( 5085)
  covalent geometry    : angle       0.61099 ( 6925)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3128.04 seconds
wall clock time: 54 minutes 47.61 seconds (3287.61 seconds total)