Starting phenix.real_space_refine
on Fri Jun  6 13:24:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u63_41942/06_2025/8u63_41942.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u63_41942/06_2025/8u63_41942.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u63_41942/06_2025/8u63_41942.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u63_41942/06_2025/8u63_41942.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u63_41942/06_2025/8u63_41942.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u63_41942/06_2025/8u63_41942.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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      46      5.16       5
     C    4894      2.51       5
     N    1350      2.21       5
     O    1468      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7758
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3836
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 465}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.44, per 1000 atoms: 1.09
  Number of scatterers: 7758
  At special positions: 0
  Unit cell: (105.777, 99.207, 106.434, 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      46     16.00
     O    1468      8.00
     N    1350      7.00
     C    4894      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1848

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 8 sheets defined
      44.6% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 15
      removed outlier: 3.613A  pdb=" N   VAL A  11 " --> pdb=" O   ASP A   7 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A  12 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 66 through 71
    Processing helix  chain 'A' and resid 71 through 82
    Processing helix  chain 'A' and resid 131 through 145
      removed outlier: 3.861A  pdb=" N   GLY A 137 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 165
    Processing helix  chain 'A' and resid 205 through 215
    Processing helix  chain 'A' and resid 253 through 263
    Processing helix  chain 'A' and resid 294 through 338
      removed outlier: 3.881A  pdb=" N   ALA A 300 " --> pdb=" O   GLU A 296 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR A 326 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS A 327 " --> pdb=" O   GLN A 323 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN A 336 " --> pdb=" O   GLN A 332 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   MET A 337 " --> pdb=" O   GLN A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 351
      removed outlier: 3.965A  pdb=" N   LEU A 349 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA A 350 " --> pdb=" O   ASP A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 361
      removed outlier: 4.063A  pdb=" N   VAL A 360 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 393
      removed outlier: 3.863A  pdb=" N   THR A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TRP A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 4.017A  pdb=" N   VAL A 408 " --> pdb=" O   HIS A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 416
      removed outlier: 3.752A  pdb=" N   GLU A 413 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ALA A 414 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR A 415 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN A 416 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 410 through 416'
    Processing helix  chain 'A' and resid 441 through 446
      removed outlier: 3.518A  pdb=" N   GLN A 444 " --> pdb=" O   GLU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 480
      removed outlier: 3.833A  pdb=" N   GLU A 474 " --> pdb=" O   ARG A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 509
      removed outlier: 3.744A  pdb=" N   ASN A 505 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 15
      removed outlier: 3.612A  pdb=" N   VAL B  11 " --> pdb=" O   ASP B   7 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU B  12 " --> pdb=" O   ALA B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 71 through 82
    Processing helix  chain 'B' and resid 131 through 145
      removed outlier: 3.861A  pdb=" N   GLY B 137 " --> pdb=" O   THR B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 165
    Processing helix  chain 'B' and resid 205 through 215
    Processing helix  chain 'B' and resid 253 through 263
    Processing helix  chain 'B' and resid 294 through 338
      removed outlier: 3.882A  pdb=" N   ALA B 300 " --> pdb=" O   GLU B 296 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   THR B 326 " --> pdb=" O   ARG B 322 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS B 327 " --> pdb=" O   GLN B 323 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLN B 336 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   MET B 337 " --> pdb=" O   GLN B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 351
      removed outlier: 3.965A  pdb=" N   LEU B 349 " --> pdb=" O   PHE B 346 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ALA B 350 " --> pdb=" O   ASP B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 361
      removed outlier: 4.062A  pdb=" N   VAL B 360 " --> pdb=" O   LEU B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 393
      removed outlier: 3.864A  pdb=" N   THR B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TRP B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 409
      removed outlier: 4.018A  pdb=" N   VAL B 408 " --> pdb=" O   HIS B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 416
      removed outlier: 3.753A  pdb=" N   GLU B 413 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ALA B 414 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR B 415 " --> pdb=" O   GLY B 412 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN B 416 " --> pdb=" O   GLU B 413 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 410 through 416'
    Processing helix  chain 'B' and resid 441 through 446
      removed outlier: 3.517A  pdb=" N   GLN B 444 " --> pdb=" O   GLU B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 480
      removed outlier: 3.834A  pdb=" N   GLU B 474 " --> pdb=" O   ARG B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 509
      removed outlier: 3.744A  pdb=" N   ASN B 505 " --> pdb=" O   SER B 501 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27
      removed outlier: 4.133A  pdb=" N   GLN A  45 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU A  33 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   GLU A 101 " --> pdb=" O   GLN A 120 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LEU A  93 " --> pdb=" O   ALA A 104 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199
      removed outlier: 5.571A  pdb=" N   VAL A 182 " --> pdb=" O   ARG A 173 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG A 173 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA A 184 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   TRP A 280 " --> pdb=" O   PHE A 174 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   LEU A 273 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   LEU A 282 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   SER A 284 " --> pdb=" O   MET A 269 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   MET A 269 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   GLY A 286 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   SER A 267 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235
      removed outlier: 3.627A  pdb=" N   GLN A 240 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 377
    Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27
      removed outlier: 4.133A  pdb=" N   GLN B  45 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU B  33 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   GLU B 101 " --> pdb=" O   GLN B 120 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   LEU B  93 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199
      removed outlier: 5.572A  pdb=" N   VAL B 182 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG B 173 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA B 184 " --> pdb=" O   ILE B 171 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   TRP B 280 " --> pdb=" O   PHE B 174 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   LEU B 273 " --> pdb=" O   TRP B 280 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   LEU B 282 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL B 271 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   SER B 284 " --> pdb=" O   MET B 269 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   MET B 269 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   GLY B 286 " --> pdb=" O   SER B 267 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   SER B 267 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 235
      removed outlier: 3.627A  pdb=" N   GLN B 240 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 372 through 377

    393 hydrogen bonds defined for protein.
    1095 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 2.77 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1437
        1.32 -     1.45: 1913
        1.45 -     1.57: 4488
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 7916
  Sorted by residual:
  bond pdb=" CA  VAL A 231 "
       pdb=" CB  VAL A 231 "
    ideal  model  delta    sigma   weight residual
    1.538  1.529  0.010 8.80e-03 1.29e+04 1.21e+00
  bond pdb=" CB  GLN B  64 "
       pdb=" CG  GLN B  64 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.53e-01
  bond pdb=" CA  VAL B 231 "
       pdb=" CB  VAL B 231 "
    ideal  model  delta    sigma   weight residual
    1.538  1.530  0.008 8.80e-03 1.29e+04 9.18e-01
  bond pdb=" CB  GLN A  64 "
       pdb=" CG  GLN A  64 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.75e-01
  bond pdb=" CB  GLN B 372 "
       pdb=" CG  GLN B 372 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.65e-01
  ... (remaining 7911 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 10570
        1.68 -     3.36: 151
        3.36 -     5.04: 29
        5.04 -     6.72: 4
        6.72 -     8.40: 6
  Bond angle restraints: 10760
  Sorted by residual:
  angle pdb=" CB  MET A 392 "
        pdb=" CG  MET A 392 "
        pdb=" SD  MET A 392 "
      ideal   model   delta    sigma   weight residual
     112.70  104.76    7.94 3.00e+00 1.11e-01 7.01e+00
  angle pdb=" CB  MET B 392 "
        pdb=" CG  MET B 392 "
        pdb=" SD  MET B 392 "
      ideal   model   delta    sigma   weight residual
     112.70  104.76    7.94 3.00e+00 1.11e-01 7.01e+00
  angle pdb=" CB  MET A 338 "
        pdb=" CG  MET A 338 "
        pdb=" SD  MET A 338 "
      ideal   model   delta    sigma   weight residual
     112.70  120.16   -7.46 3.00e+00 1.11e-01 6.19e+00
  angle pdb=" CB  MET B 338 "
        pdb=" CG  MET B 338 "
        pdb=" SD  MET B 338 "
      ideal   model   delta    sigma   weight residual
     112.70  120.16   -7.46 3.00e+00 1.11e-01 6.18e+00
  angle pdb=" CA  MET A 392 "
        pdb=" CB  MET A 392 "
        pdb=" CG  MET A 392 "
      ideal   model   delta    sigma   weight residual
     114.10  119.07   -4.97 2.00e+00 2.50e-01 6.17e+00
  ... (remaining 10755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4100
       17.73 -    35.46: 510
       35.46 -    53.19: 130
       53.19 -    70.92: 44
       70.92 -    88.65: 18
  Dihedral angle restraints: 4802
    sinusoidal: 1954
      harmonic: 2848
  Sorted by residual:
  dihedral pdb=" CA  ARG A 324 "
           pdb=" C   ARG A 324 "
           pdb=" N   GLU A 325 "
           pdb=" CA  GLU A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.02   15.98     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  ARG B 324 "
           pdb=" C   ARG B 324 "
           pdb=" N   GLU B 325 "
           pdb=" CA  GLU B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.06   15.94     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CG  ARG B 386 "
           pdb=" CD  ARG B 386 "
           pdb=" NE  ARG B 386 "
           pdb=" CZ  ARG B 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.59  -43.59     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 4799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 715
       0.027 -    0.054: 298
       0.054 -    0.081: 106
       0.081 -    0.108: 67
       0.108 -    0.135: 22
  Chirality restraints: 1208
  Sorted by residual:
  chirality pdb=" CA  ILE B 220 "
            pdb=" N   ILE B 220 "
            pdb=" C   ILE B 220 "
            pdb=" CB  ILE B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  ILE A 220 "
            pdb=" N   ILE A 220 "
            pdb=" C   ILE A 220 "
            pdb=" CB  ILE A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  VAL B  53 "
            pdb=" N   VAL B  53 "
            pdb=" C   VAL B  53 "
            pdb=" CB  VAL B  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.14e-01
  ... (remaining 1205 not shown)

  Planarity restraints: 1402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 231 "    0.030 5.00e-02 4.00e+02   4.57e-02 3.34e+00
        pdb=" N   PRO B 232 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 232 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 232 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 231 "    0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO A 232 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 232 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 232 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 289 "   -0.022 5.00e-02 4.00e+02   3.34e-02 1.79e+00
        pdb=" N   PRO A 290 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 290 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 290 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1399 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 178
        2.70 -     3.25: 7408
        3.25 -     3.80: 12140
        3.80 -     4.35: 15907
        4.35 -     4.90: 26649
  Nonbonded interactions: 62282
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  65 "
            pdb=" OD1 ASP A  67 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" OD1 ASP B  67 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" O   SER A 309 "
            pdb=" OG  SER A 313 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   SER B 309 "
            pdb=" OG  SER B 313 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   GLY A 305 "
            pdb=" OG  SER A 309 "
     model   vdw
     2.276 3.040
  ... (remaining 62277 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     26.190
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7918  Z= 0.162
  Angle     :  0.559   8.401  10760  Z= 0.278
  Chirality :  0.041   0.135   1208
  Planarity :  0.004   0.046   1402
  Dihedral  : 17.941  88.648   2954
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 27.62 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.74 (0.25), residues: 972
  helix: -0.09 (0.24), residues: 400
  sheet: -0.28 (0.36), residues: 164
  loop : -0.84 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 280 
 HIS   0.011   0.001   HIS A 295 
 PHE   0.009   0.001   PHE A 199 
 TYR   0.023   0.002   TYR B 225 
 ARG   0.007   0.001   ARG B 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20424 (  393)
  hydrogen bonds       : angle       7.51952 ( 1095)
  covalent geometry    : bond        0.00284 ( 7916)
  covalent geometry    : angle       0.55858 (10760)
  Misc. bond           : bond        0.06334 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 197
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 THR cc_start: 0.8300 (p) cc_final: 0.8075 (p)
REVERT: A  333 GLN cc_start: 0.7942 (tt0) cc_final: 0.7671 (tt0)
REVERT: A  480 MET cc_start: 0.8073 (mmm) cc_final: 0.7658 (tpp)
REVERT: B   79 ARG cc_start: 0.7718 (mmt180) cc_final: 0.7483 (mmt-90)
REVERT: B  372 GLN cc_start: 0.7405 (tm-30) cc_final: 0.7139 (tm-30)
REVERT: B  435 VAL cc_start: 0.8460 (m) cc_final: 0.8117 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 197
  average time/residue: 0.2643
  time to fit residues: 65.6146
Evaluate side-chains
  189 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  489 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0980
   chunk 50 optimal weight:    0.2980
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 306 GLN
A 433 ASN
B 262 ASN
B 302 GLN
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.150151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130397 restraints weight = 10652.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.18
r_work: 0.3507 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7918  Z= 0.152
  Angle     :  0.576   8.476  10760  Z= 0.285
  Chirality :  0.042   0.141   1208
  Planarity :  0.005   0.041   1402
  Dihedral  :  5.819  55.617   1104
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 24.64 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.23 (0.26), residues: 972
  helix:  1.03 (0.25), residues: 408
  sheet:  0.28 (0.37), residues: 160
  loop : -0.74 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 280 
 HIS   0.010   0.002   HIS A 295 
 PHE   0.012   0.002   PHE A 199 
 TYR   0.009   0.001   TYR A 400 
 ARG   0.007   0.001   ARG A 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  393)
  hydrogen bonds       : angle       5.12305 ( 1095)
  covalent geometry    : bond        0.00350 ( 7916)
  covalent geometry    : angle       0.57625 (10760)
  Misc. bond           : bond        0.00012 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8586 (m) cc_final: 0.8322 (t)
REVERT: A  139 MET cc_start: 0.6913 (mtm) cc_final: 0.6712 (mtm)
REVERT: A  154 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7176 (mt-10)
REVERT: A  164 THR cc_start: 0.8381 (p) cc_final: 0.8128 (p)
REVERT: A  167 ASP cc_start: 0.8160 (m-30) cc_final: 0.7831 (m-30)
REVERT: A  206 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7255 (tp30)
REVERT: A  308 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7656 (mp)
REVERT: A  319 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6715 (tm-30)
REVERT: B   64 GLN cc_start: 0.6951 (mp10) cc_final: 0.6623 (mp10)
REVERT: B   94 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8149 (mp)
REVERT: B  139 MET cc_start: 0.7280 (mtm) cc_final: 0.6892 (mtm)
REVERT: B  337 MET cc_start: 0.7519 (mpm) cc_final: 0.7307 (mpm)
  outliers start: 20
  outliers final: 7
  residues processed: 214
  average time/residue: 0.2668
  time to fit residues: 73.1619
Evaluate side-chains
  203 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 194
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  369 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0370
   chunk 17 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0670
   chunk 21 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 306 GLN
A 351 GLN
A 433 ASN
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 262 ASN
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.150272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130295 restraints weight = 10798.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.20
r_work: 0.3508 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7918  Z= 0.143
  Angle     :  0.546   8.063  10760  Z= 0.270
  Chirality :  0.042   0.139   1208
  Planarity :  0.005   0.044   1402
  Dihedral  :  5.625  56.597   1102
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.00 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.56 (0.26), residues: 972
  helix:  1.42 (0.25), residues: 406
  sheet:  0.42 (0.38), residues: 160
  loop : -0.69 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 437 
 HIS   0.010   0.001   HIS B 295 
 PHE   0.011   0.001   PHE A 199 
 TYR   0.007   0.001   TYR A 400 
 ARG   0.010   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03511 (  393)
  hydrogen bonds       : angle       4.79206 ( 1095)
  covalent geometry    : bond        0.00332 ( 7916)
  covalent geometry    : angle       0.54595 (10760)
  Misc. bond           : bond        0.00029 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 200
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8589 (m) cc_final: 0.8314 (t)
REVERT: A  139 MET cc_start: 0.7072 (mtm) cc_final: 0.6409 (mtm)
REVERT: A  154 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7047 (mt-10)
REVERT: A  163 MET cc_start: 0.7984 (mtp) cc_final: 0.7766 (ttm)
REVERT: A  164 THR cc_start: 0.8402 (p) cc_final: 0.8186 (p)
REVERT: A  304 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8228 (mt)
REVERT: A  337 MET cc_start: 0.6900 (mpm) cc_final: 0.6589 (mpm)
REVERT: B   64 GLN cc_start: 0.6986 (mp10) cc_final: 0.6780 (mp10)
REVERT: B  139 MET cc_start: 0.7215 (mtm) cc_final: 0.6902 (mtm)
REVERT: B  316 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6905 (mt-10)
REVERT: B  422 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7954 (t)
  outliers start: 26
  outliers final: 14
  residues processed: 214
  average time/residue: 0.2359
  time to fit residues: 64.8326
Evaluate side-chains
  209 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  489 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  422 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 61 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 90 optimal weight:    0.0970
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 120 GLN
B 262 ASN
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.149594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.128906 restraints weight = 10719.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.24
r_work: 0.3487 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7918  Z= 0.171
  Angle     :  0.577   8.965  10760  Z= 0.279
  Chirality :  0.043   0.140   1208
  Planarity :  0.005   0.052   1402
  Dihedral  :  5.692  54.960   1102
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 25.71 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.70 (0.27), residues: 972
  helix:  1.59 (0.26), residues: 404
  sheet:  0.51 (0.39), residues: 160
  loop : -0.67 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 391 
 HIS   0.008   0.001   HIS B 295 
 PHE   0.012   0.002   PHE A 199 
 TYR   0.007   0.001   TYR B 172 
 ARG   0.009   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03351 (  393)
  hydrogen bonds       : angle       4.67646 ( 1095)
  covalent geometry    : bond        0.00399 ( 7916)
  covalent geometry    : angle       0.57687 (10760)
  Misc. bond           : bond        0.00032 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 196
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8643 (m) cc_final: 0.8345 (t)
REVERT: A  139 MET cc_start: 0.7269 (mtm) cc_final: 0.6518 (mtm)
REVERT: A  154 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6995 (mt-10)
REVERT: A  163 MET cc_start: 0.8048 (mtp) cc_final: 0.7787 (ttm)
REVERT: A  304 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8210 (mt)
REVERT: A  337 MET cc_start: 0.7020 (mpm) cc_final: 0.6698 (mpm)
REVERT: B   94 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8127 (mp)
REVERT: B  139 MET cc_start: 0.7179 (mtm) cc_final: 0.6855 (mtm)
REVERT: B  158 ARG cc_start: 0.7641 (tpm170) cc_final: 0.7414 (tpm170)
REVERT: B  316 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7023 (mt-10)
REVERT: B  422 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7967 (t)
REVERT: B  435 VAL cc_start: 0.8588 (m) cc_final: 0.8371 (p)
  outliers start: 27
  outliers final: 14
  residues processed: 211
  average time/residue: 0.2246
  time to fit residues: 61.8116
Evaluate side-chains
  216 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 199
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  422 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0980
   chunk 10 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 ASN
A 306 GLN
A 351 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
B 306 GLN
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.149571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.129357 restraints weight = 10678.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.19
r_work: 0.3495 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7918  Z= 0.187
  Angle     :  0.584   9.435  10760  Z= 0.284
  Chirality :  0.043   0.140   1208
  Planarity :  0.005   0.041   1402
  Dihedral  :  5.726  54.116   1102
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 26.79 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.79 (0.27), residues: 972
  helix:  1.61 (0.26), residues: 406
  sheet:  0.54 (0.39), residues: 160
  loop : -0.57 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 280 
 HIS   0.008   0.001   HIS B 295 
 PHE   0.013   0.002   PHE A  34 
 TYR   0.007   0.001   TYR A 415 
 ARG   0.009   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  393)
  hydrogen bonds       : angle       4.66080 ( 1095)
  covalent geometry    : bond        0.00438 ( 7916)
  covalent geometry    : angle       0.58420 (10760)
  Misc. bond           : bond        0.00028 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 202
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8687 (m) cc_final: 0.8394 (t)
REVERT: A  139 MET cc_start: 0.7312 (mtm) cc_final: 0.6559 (mtm)
REVERT: A  154 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6926 (mt-10)
REVERT: A  163 MET cc_start: 0.8054 (mtp) cc_final: 0.7848 (ttm)
REVERT: A  319 GLU cc_start: 0.7605 (mm-30) cc_final: 0.6860 (tm-30)
REVERT: A  337 MET cc_start: 0.7068 (mpm) cc_final: 0.6775 (mpm)
REVERT: A  371 ARG cc_start: 0.7560 (tpt90) cc_final: 0.7344 (tpt170)
REVERT: B   94 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8113 (mp)
REVERT: B  139 MET cc_start: 0.7191 (mtm) cc_final: 0.6820 (mtm)
REVERT: B  158 ARG cc_start: 0.7660 (tpm170) cc_final: 0.7437 (tpm170)
REVERT: B  273 LEU cc_start: 0.8509 (mt) cc_final: 0.8232 (mp)
REVERT: B  316 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7046 (mt-10)
REVERT: B  324 ARG cc_start: 0.8249 (ptm160) cc_final: 0.7918 (ptm160)
REVERT: B  435 VAL cc_start: 0.8587 (m) cc_final: 0.8341 (p)
  outliers start: 24
  outliers final: 19
  residues processed: 217
  average time/residue: 0.3139
  time to fit residues: 88.8415
Evaluate side-chains
  214 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 194
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  240 GLN
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   chunk 87 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
A 351 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
B 389 HIS
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.150313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.129953 restraints weight = 10530.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.21
r_work: 0.3502 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7918  Z= 0.140
  Angle     :  0.559   9.244  10760  Z= 0.274
  Chirality :  0.042   0.138   1208
  Planarity :  0.005   0.048   1402
  Dihedral  :  5.689  55.850   1102
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 26.79 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.92 (0.27), residues: 972
  helix:  1.81 (0.26), residues: 404
  sheet:  0.52 (0.39), residues: 160
  loop : -0.55 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 391 
 HIS   0.008   0.001   HIS B 295 
 PHE   0.011   0.001   PHE B  34 
 TYR   0.008   0.001   TYR B 172 
 ARG   0.007   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03089 (  393)
  hydrogen bonds       : angle       4.54988 ( 1095)
  covalent geometry    : bond        0.00330 ( 7916)
  covalent geometry    : angle       0.55920 (10760)
  Misc. bond           : bond        0.00030 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 201
  time to evaluate  : 2.172 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8642 (m) cc_final: 0.8374 (t)
REVERT: A  139 MET cc_start: 0.7344 (mtm) cc_final: 0.6566 (mtm)
REVERT: A  154 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6897 (mt-10)
REVERT: A  163 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7860 (ttm)
REVERT: A  288 ARG cc_start: 0.8768 (mpp80) cc_final: 0.8540 (mpp80)
REVERT: A  319 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6843 (tm-30)
REVERT: A  337 MET cc_start: 0.7076 (mpm) cc_final: 0.6775 (mpm)
REVERT: A  371 ARG cc_start: 0.7532 (tpt90) cc_final: 0.7318 (tpt170)
REVERT: B   94 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8097 (mp)
REVERT: B  158 ARG cc_start: 0.7610 (tpm170) cc_final: 0.7379 (tpm170)
REVERT: B  273 LEU cc_start: 0.8498 (mt) cc_final: 0.8215 (mp)
REVERT: B  316 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7019 (mt-10)
REVERT: B  324 ARG cc_start: 0.8206 (ptm160) cc_final: 0.7873 (ptm160)
REVERT: B  435 VAL cc_start: 0.8573 (m) cc_final: 0.8321 (p)
  outliers start: 26
  outliers final: 20
  residues processed: 215
  average time/residue: 0.3950
  time to fit residues: 110.3274
Evaluate side-chains
  214 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 192
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  192 GLU
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 12 optimal weight:    7.9990
   chunk 69 optimal weight:    0.0970
   chunk 89 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   chunk 71 optimal weight:    0.4980
   chunk 20 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.149411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.129110 restraints weight = 10751.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.19
r_work: 0.3486 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7918  Z= 0.177
  Angle     :  0.589  10.750  10760  Z= 0.286
  Chirality :  0.044   0.170   1208
  Planarity :  0.005   0.061   1402
  Dihedral  :  5.730  54.588   1102
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 26.43 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.91 (0.27), residues: 972
  helix:  1.77 (0.26), residues: 406
  sheet:  0.54 (0.39), residues: 160
  loop : -0.55 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 391 
 HIS   0.009   0.001   HIS B 295 
 PHE   0.011   0.002   PHE A  34 
 TYR   0.009   0.001   TYR B 172 
 ARG   0.008   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03247 (  393)
  hydrogen bonds       : angle       4.58433 ( 1095)
  covalent geometry    : bond        0.00417 ( 7916)
  covalent geometry    : angle       0.58910 (10760)
  Misc. bond           : bond        0.00029 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 198
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8687 (m) cc_final: 0.8409 (t)
REVERT: A  139 MET cc_start: 0.7358 (mtm) cc_final: 0.6592 (mtm)
REVERT: A  154 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6928 (mt-10)
REVERT: A  163 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7875 (ttm)
REVERT: A  319 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6880 (tm-30)
REVERT: A  337 MET cc_start: 0.7135 (mpm) cc_final: 0.6804 (mpm)
REVERT: B   94 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8086 (mp)
REVERT: B  158 ARG cc_start: 0.7614 (tpm170) cc_final: 0.7392 (tpm170)
REVERT: B  273 LEU cc_start: 0.8510 (mt) cc_final: 0.8232 (mp)
REVERT: B  316 GLU cc_start: 0.7226 (mt-10) cc_final: 0.7006 (mt-10)
REVERT: B  324 ARG cc_start: 0.8208 (ptm160) cc_final: 0.7863 (ptm160)
REVERT: B  435 VAL cc_start: 0.8610 (m) cc_final: 0.8365 (p)
  outliers start: 28
  outliers final: 22
  residues processed: 215
  average time/residue: 0.2311
  time to fit residues: 64.0646
Evaluate side-chains
  222 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 198
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0770
   chunk 7 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5736

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.148876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.128120 restraints weight = 10674.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.23
r_work: 0.3478 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7918  Z= 0.196
  Angle     :  0.603  10.551  10760  Z= 0.293
  Chirality :  0.044   0.164   1208
  Planarity :  0.005   0.054   1402
  Dihedral  :  5.784  53.591   1102
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 26.31 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.92 (0.27), residues: 972
  helix:  1.78 (0.26), residues: 408
  sheet:  0.48 (0.39), residues: 160
  loop : -0.51 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 391 
 HIS   0.009   0.001   HIS B 295 
 PHE   0.012   0.002   PHE A 199 
 TYR   0.008   0.001   TYR A 415 
 ARG   0.010   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03325 (  393)
  hydrogen bonds       : angle       4.63044 ( 1095)
  covalent geometry    : bond        0.00461 ( 7916)
  covalent geometry    : angle       0.60339 (10760)
  Misc. bond           : bond        0.00028 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 200
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8723 (m) cc_final: 0.8440 (t)
REVERT: A  154 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6961 (mt-10)
REVERT: A  319 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6897 (tm-30)
REVERT: A  337 MET cc_start: 0.7134 (mpm) cc_final: 0.6825 (mpm)
REVERT: B   94 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8086 (mp)
REVERT: B  158 ARG cc_start: 0.7631 (tpm170) cc_final: 0.7429 (tpm170)
REVERT: B  273 LEU cc_start: 0.8515 (mt) cc_final: 0.8243 (mp)
REVERT: B  316 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7027 (mt-10)
REVERT: B  324 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7889 (ptm160)
REVERT: B  435 VAL cc_start: 0.8612 (m) cc_final: 0.8378 (p)
  outliers start: 26
  outliers final: 25
  residues processed: 214
  average time/residue: 0.2462
  time to fit residues: 67.7024
Evaluate side-chains
  223 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 197
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  240 GLN
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    0.0030
   chunk 43 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 92 optimal weight:    0.4980
   chunk 97 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0370
   overall best weight:    0.4268

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.149252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.128762 restraints weight = 10803.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.23
r_work: 0.3491 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7918  Z= 0.158
  Angle     :  0.586   9.361  10760  Z= 0.284
  Chirality :  0.043   0.151   1208
  Planarity :  0.005   0.049   1402
  Dihedral  :  5.742  55.364   1102
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 26.90 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.01 (0.27), residues: 972
  helix:  1.87 (0.26), residues: 408
  sheet:  0.29 (0.38), residues: 170
  loop : -0.39 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 391 
 HIS   0.010   0.001   HIS B 295 
 PHE   0.011   0.001   PHE A  34 
 TYR   0.008   0.001   TYR B 172 
 ARG   0.007   0.001   ARG B 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03187 (  393)
  hydrogen bonds       : angle       4.55547 ( 1095)
  covalent geometry    : bond        0.00373 ( 7916)
  covalent geometry    : angle       0.58581 (10760)
  Misc. bond           : bond        0.00030 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 201
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8697 (m) cc_final: 0.8425 (t)
REVERT: A  154 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7005 (mt-10)
REVERT: A  163 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7858 (ttm)
REVERT: A  304 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8198 (mt)
REVERT: A  319 GLU cc_start: 0.7582 (mm-30) cc_final: 0.6868 (tm-30)
REVERT: B   94 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8075 (mp)
REVERT: B  158 ARG cc_start: 0.7623 (tpm170) cc_final: 0.7415 (tpm170)
REVERT: B  273 LEU cc_start: 0.8509 (mt) cc_final: 0.8228 (mp)
REVERT: B  316 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7065 (mt-10)
REVERT: B  324 ARG cc_start: 0.8248 (ptm160) cc_final: 0.7925 (ptm160)
REVERT: B  435 VAL cc_start: 0.8578 (m) cc_final: 0.8351 (p)
  outliers start: 25
  outliers final: 21
  residues processed: 214
  average time/residue: 0.2314
  time to fit residues: 63.7300
Evaluate side-chains
  222 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 198
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0770
   chunk 59 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 52 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 120 GLN
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.148805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.128256 restraints weight = 10758.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.23
r_work: 0.3482 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7918  Z= 0.194
  Angle     :  0.614  10.823  10760  Z= 0.297
  Chirality :  0.044   0.154   1208
  Planarity :  0.005   0.049   1402
  Dihedral  :  5.796  54.187   1102
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 27.02 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.96 (0.27), residues: 972
  helix:  1.79 (0.26), residues: 408
  sheet:  0.43 (0.39), residues: 160
  loop : -0.44 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 391 
 HIS   0.011   0.001   HIS B 295 
 PHE   0.012   0.002   PHE A  34 
 TYR   0.008   0.001   TYR A 415 
 ARG   0.009   0.001   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03319 (  393)
  hydrogen bonds       : angle       4.61510 ( 1095)
  covalent geometry    : bond        0.00457 ( 7916)
  covalent geometry    : angle       0.61438 (10760)
  Misc. bond           : bond        0.00029 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6951 (mt-10)
REVERT: A  163 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7858 (ttm)
REVERT: A  304 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (mt)
REVERT: A  319 GLU cc_start: 0.7610 (mm-30) cc_final: 0.6886 (tm-30)
REVERT: B   94 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8088 (mp)
REVERT: B  273 LEU cc_start: 0.8513 (mt) cc_final: 0.8235 (mp)
REVERT: B  316 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7056 (mt-10)
REVERT: B  435 VAL cc_start: 0.8612 (m) cc_final: 0.8379 (p)
  outliers start: 26
  outliers final: 23
  residues processed: 213
  average time/residue: 0.2346
  time to fit residues: 64.8791
Evaluate side-chains
  220 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 194
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0000
   chunk 58 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.127940 restraints weight = 10716.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.21
r_work: 0.3483 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7918  Z= 0.210
  Angle     :  0.625  11.308  10760  Z= 0.302
  Chirality :  0.045   0.159   1208
  Planarity :  0.005   0.049   1402
  Dihedral  :  5.829  53.550   1102
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 27.26 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.92 (0.27), residues: 972
  helix:  1.74 (0.26), residues: 408
  sheet:  0.40 (0.39), residues: 160
  loop : -0.44 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 391 
 HIS   0.011   0.001   HIS B 295 
 PHE   0.013   0.002   PHE B 199 
 TYR   0.008   0.001   TYR A 415 
 ARG   0.010   0.001   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03387 (  393)
  hydrogen bonds       : angle       4.64162 ( 1095)
  covalent geometry    : bond        0.00497 ( 7916)
  covalent geometry    : angle       0.62513 (10760)
  Misc. bond           : bond        0.00028 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5618.38 seconds
wall clock time: 99 minutes 26.78 seconds (5966.78 seconds total)