Starting phenix.real_space_refine
on Fri Oct 10 16:43:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u63_41942/10_2025/8u63_41942.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u63_41942/10_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_41942/10_2025/8u63_41942.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u63_41942/10_2025/8u63_41942.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u63_41942/10_2025/8u63_41942.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u63_41942/10_2025/8u63_41942.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.97, per 1000 atoms: 0.38
  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: 0.72
  Conformation dependent library (CDL) restraints added in 449.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.31
  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: 1.28

  Time building geometry restraints manager: 0.95 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: 0.01
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:             10.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.320
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.370
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.001   ARG B 324 
 TYR   0.023   0.002   TYR B 225 
 PHE   0.009   0.001   PHE A 199 
 TRP   0.010   0.001   TRP A 280 
 HIS   0.011   0.001   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7916)
  covalent geometry    : angle       0.55858 (10760)
  hydrogen bonds       : bond        0.20424 (  393)
  hydrogen bonds       : angle       7.51952 ( 1095)
  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  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 THR cc_start: 0.8300 (p) cc_final: 0.8076 (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: 0.1198
  time to fit residues: 29.7601
Evaluate side-chains
  188 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 187
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0000
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.5984

-------------------------------------------------------------------------------
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 = 0.3886 r_free = 0.3886 target = 0.148820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129059 restraints weight = 10690.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.16
r_work: 0.3490 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1256

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= 0.209
  Angle     :  0.616   9.723  10760  Z= 0.304
  Chirality :  0.044   0.147   1208
  Planarity :  0.005   0.041   1402
  Dihedral  :  5.906  54.163   1104
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 24.29 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.26), residues: 972
  helix:  1.02 (0.25), residues: 406
  sheet:  0.20 (0.37), residues: 162
  loop : -0.80 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 324 
 TYR   0.009   0.002   TYR A 153 
 PHE   0.015   0.002   PHE A 199 
 TRP   0.010   0.002   TRP A 280 
 HIS   0.010   0.002   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 7916)
  covalent geometry    : angle       0.61625 (10760)
  hydrogen bonds       : bond        0.04105 (  393)
  hydrogen bonds       : angle       5.16695 ( 1095)
  Misc. bond           : bond        0.00014 (    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
  229 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7866 (ttt180)
REVERT: A   96 SER cc_start: 0.8679 (m) cc_final: 0.8386 (t)
REVERT: A  139 MET cc_start: 0.7020 (mtm) cc_final: 0.6210 (mtm)
REVERT: A  154 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7180 (mt-10)
REVERT: A  163 MET cc_start: 0.8015 (mtp) cc_final: 0.7495 (mtt)
REVERT: A  164 THR cc_start: 0.8441 (p) cc_final: 0.8202 (p)
REVERT: A  206 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7243 (tp30)
REVERT: A  304 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8185 (mt)
REVERT: A  308 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7642 (mp)
REVERT: B   94 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8150 (mp)
REVERT: B  139 MET cc_start: 0.7262 (mtm) cc_final: 0.6931 (mtm)
REVERT: B  337 MET cc_start: 0.7524 (mpm) cc_final: 0.7303 (mpm)
  outliers start: 26
  outliers final: 11
  residues processed: 221
  average time/residue: 0.1119
  time to fit residues: 31.5462
Evaluate side-chains
  204 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 190
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  408 VAL
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  159 GLU
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  408 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0060
   chunk 73 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7598

-------------------------------------------------------------------------------
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 351 GLN
A 433 ASN
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 262 ASN
B 306 GLN
B 433 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.148575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.128603 restraints weight = 10624.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.16
r_work: 0.3481 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   7918  Z= 0.249
  Angle     :  0.624   9.867  10760  Z= 0.306
  Chirality :  0.045   0.153   1208
  Planarity :  0.005   0.051   1402
  Dihedral  :  5.862  52.643   1102
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 24.40 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.26), residues: 972
  helix:  1.23 (0.25), residues: 406
  sheet:  0.33 (0.37), residues: 162
  loop : -0.83 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 386 
 TYR   0.009   0.002   TYR A 415 
 PHE   0.015   0.002   PHE A 199 
 TRP   0.009   0.002   TRP A 391 
 HIS   0.009   0.002   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 ( 7916)
  covalent geometry    : angle       0.62373 (10760)
  hydrogen bonds       : bond        0.04008 (  393)
  hydrogen bonds       : angle       4.97202 ( 1095)
  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
  231 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 198
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 MET cc_start: 0.7259 (mtm) cc_final: 0.6489 (mtm)
REVERT: A  154 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7013 (mt-10)
REVERT: A  163 MET cc_start: 0.8101 (mtp) cc_final: 0.7665 (mtt)
REVERT: A  164 THR cc_start: 0.8421 (p) cc_final: 0.8197 (p)
REVERT: A  167 ASP cc_start: 0.8142 (m-30) cc_final: 0.7879 (m-30)
REVERT: A  304 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8213 (mt)
REVERT: A  319 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6796 (tm-30)
REVERT: A  337 MET cc_start: 0.6944 (mpm) cc_final: 0.6647 (mpm)
REVERT: B   94 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8142 (mp)
REVERT: B  139 MET cc_start: 0.7274 (mtm) cc_final: 0.6890 (mtm)
REVERT: B  163 MET cc_start: 0.7948 (mtp) cc_final: 0.7652 (mtp)
REVERT: B  316 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7028 (mt-10)
REVERT: B  324 ARG cc_start: 0.8218 (ptm160) cc_final: 0.7857 (ptm160)
  outliers start: 33
  outliers final: 16
  residues processed: 220
  average time/residue: 0.0977
  time to fit residues: 27.9507
Evaluate side-chains
  209 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
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  284 SER
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  408 VAL
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  369 GLU
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  485 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 25 optimal weight:    0.3980
   chunk 96 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0170
   chunk 73 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A  64 GLN
A 120 GLN
A 306 GLN
A 433 ASN
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 262 ASN
B 306 GLN
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 433 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.149358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.129238 restraints weight = 10812.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.21
r_work: 0.3491 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7918  Z= 0.167
  Angle     :  0.568   9.229  10760  Z= 0.279
  Chirality :  0.042   0.138   1208
  Planarity :  0.005   0.049   1402
  Dihedral  :  5.763  54.640   1102
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.71 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 972
  helix:  1.46 (0.25), residues: 408
  sheet:  0.43 (0.38), residues: 160
  loop : -0.70 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 386 
 TYR   0.008   0.001   TYR B 172 
 PHE   0.011   0.002   PHE A 199 
 TRP   0.008   0.001   TRP A 391 
 HIS   0.007   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 7916)
  covalent geometry    : angle       0.56815 (10760)
  hydrogen bonds       : bond        0.03393 (  393)
  hydrogen bonds       : angle       4.72989 ( 1095)
  Misc. bond           : bond        0.00031 (    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
  219 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 193
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8698 (m) cc_final: 0.8418 (t)
REVERT: A  139 MET cc_start: 0.7303 (mtm) cc_final: 0.6512 (mtm)
REVERT: A  154 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6930 (mt-10)
REVERT: A  163 MET cc_start: 0.8065 (mtp) cc_final: 0.7821 (ttm)
REVERT: A  167 ASP cc_start: 0.8108 (m-30) cc_final: 0.7848 (m-30)
REVERT: A  246 PHE cc_start: 0.8896 (m-80) cc_final: 0.8664 (m-80)
REVERT: A  304 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8253 (mt)
REVERT: A  319 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6834 (tm-30)
REVERT: A  337 MET cc_start: 0.7008 (mpm) cc_final: 0.6693 (mpm)
REVERT: B  139 MET cc_start: 0.7242 (mtm) cc_final: 0.6819 (mtm)
REVERT: B  273 LEU cc_start: 0.8523 (mt) cc_final: 0.8251 (mp)
REVERT: B  316 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7074 (mt-10)
REVERT: B  435 VAL cc_start: 0.8570 (m) cc_final: 0.8343 (p)
  outliers start: 26
  outliers final: 18
  residues processed: 211
  average time/residue: 0.1056
  time to fit residues: 29.0552
Evaluate side-chains
  210 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 191
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  304 ILE
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 96 optimal weight:    0.2980
   chunk 19 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 92 optimal weight:    0.1980
   chunk 58 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  64 GLN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 ASN
A 306 GLN
A 505 ASN
B 120 GLN
B 306 GLN
B 389 HIS
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.149425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.129369 restraints weight = 10694.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 2.19
r_work: 0.3488 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2032

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= 0.193
  Angle     :  0.591  10.479  10760  Z= 0.288
  Chirality :  0.043   0.139   1208
  Planarity :  0.005   0.051   1402
  Dihedral  :  5.783  53.514   1102
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 26.07 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.27), residues: 972
  helix:  1.54 (0.25), residues: 408
  sheet:  0.43 (0.38), residues: 160
  loop : -0.66 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 324 
 TYR   0.009   0.001   TYR B 172 
 PHE   0.012   0.002   PHE A 199 
 TRP   0.008   0.001   TRP B 280 
 HIS   0.008   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 7916)
  covalent geometry    : angle       0.59112 (10760)
  hydrogen bonds       : bond        0.03430 (  393)
  hydrogen bonds       : angle       4.69381 ( 1095)
  Misc. bond           : bond        0.00030 (    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
  225 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLN cc_start: 0.7488 (mp10) cc_final: 0.7146 (mp10)
REVERT: A   96 SER cc_start: 0.8729 (m) cc_final: 0.8448 (t)
REVERT: A  139 MET cc_start: 0.7342 (mtm) cc_final: 0.6555 (mtm)
REVERT: A  154 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6948 (mt-10)
REVERT: A  163 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7902 (ttm)
REVERT: A  319 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6858 (tm-30)
REVERT: A  337 MET cc_start: 0.7041 (mpm) cc_final: 0.6763 (mpm)
REVERT: B   94 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8099 (mp)
REVERT: B  139 MET cc_start: 0.7214 (mtm) cc_final: 0.6879 (mtm)
REVERT: B  316 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7067 (mt-10)
REVERT: B  324 ARG cc_start: 0.8275 (ptm160) cc_final: 0.8060 (ptm160)
REVERT: B  435 VAL cc_start: 0.8571 (m) cc_final: 0.8319 (p)
  outliers start: 28
  outliers final: 19
  residues processed: 214
  average time/residue: 0.1143
  time to fit residues: 31.5423
Evaluate side-chains
  217 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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  369 GLU
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  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 95 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 89 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
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 = 0.3870 r_free = 0.3870 target = 0.147960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.127294 restraints weight = 10653.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.22
r_work: 0.3465 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7918  Z= 0.236
  Angle     :  0.622  11.177  10760  Z= 0.303
  Chirality :  0.045   0.147   1208
  Planarity :  0.005   0.062   1402
  Dihedral  :  5.877  51.731   1102
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 25.60 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.27), residues: 972
  helix:  1.54 (0.25), residues: 406
  sheet:  0.39 (0.38), residues: 160
  loop : -0.66 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 386 
 TYR   0.009   0.002   TYR A 415 
 PHE   0.014   0.002   PHE A 194 
 TRP   0.012   0.002   TRP A 391 
 HIS   0.008   0.002   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 7916)
  covalent geometry    : angle       0.62167 (10760)
  hydrogen bonds       : bond        0.03581 (  393)
  hydrogen bonds       : angle       4.75688 ( 1095)
  Misc. bond           : bond        0.00028 (    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
  229 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 200
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6976 (mt-10)
REVERT: A  319 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6863 (tm-30)
REVERT: B   79 ARG cc_start: 0.8104 (mmt90) cc_final: 0.7825 (mtt-85)
REVERT: B   94 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8121 (mp)
REVERT: B  139 MET cc_start: 0.7280 (mtm) cc_final: 0.6961 (mtm)
REVERT: B  158 ARG cc_start: 0.7613 (tpm170) cc_final: 0.7377 (tpm170)
REVERT: B  266 LEU cc_start: 0.8710 (mt) cc_final: 0.8472 (mt)
REVERT: B  273 LEU cc_start: 0.8533 (mt) cc_final: 0.8268 (mp)
REVERT: B  316 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6967 (mt-10)
REVERT: B  324 ARG cc_start: 0.8288 (ptm160) cc_final: 0.8054 (ptm160)
REVERT: B  435 VAL cc_start: 0.8611 (m) cc_final: 0.8356 (p)
  outliers start: 29
  outliers final: 24
  residues processed: 215
  average time/residue: 0.1170
  time to fit residues: 32.3278
Evaluate side-chains
  221 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 196
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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  228 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  291 LEU
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  308 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 38 optimal weight:    0.3980
   chunk 79 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 36 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
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 = 0.3875 r_free = 0.3875 target = 0.148297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.127539 restraints weight = 10604.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.21
r_work: 0.3474 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2220

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= 0.213
  Angle     :  0.612  11.419  10760  Z= 0.298
  Chirality :  0.044   0.155   1208
  Planarity :  0.005   0.042   1402
  Dihedral  :  5.845  52.479   1102
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 26.67 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.27), residues: 972
  helix:  1.62 (0.26), residues: 406
  sheet:  0.35 (0.38), residues: 160
  loop : -0.61 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 386 
 TYR   0.009   0.002   TYR A 415 
 PHE   0.013   0.002   PHE B 199 
 TRP   0.013   0.002   TRP A 391 
 HIS   0.008   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 7916)
  covalent geometry    : angle       0.61218 (10760)
  hydrogen bonds       : bond        0.03499 (  393)
  hydrogen bonds       : angle       4.70658 ( 1095)
  Misc. bond           : bond        0.00028 (    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
  234 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 201
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7000 (mt-10)
REVERT: A  163 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7879 (ttm)
REVERT: A  304 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8249 (mt)
REVERT: A  319 GLU cc_start: 0.7625 (mm-30) cc_final: 0.6878 (tm-30)
REVERT: A  324 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7061 (ttm170)
REVERT: A  391 TRP cc_start: 0.7452 (t60) cc_final: 0.6949 (t60)
REVERT: B   94 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8103 (mp)
REVERT: B  139 MET cc_start: 0.7297 (mtm) cc_final: 0.6939 (mtm)
REVERT: B  158 ARG cc_start: 0.7585 (tpm170) cc_final: 0.7356 (tpm170)
REVERT: B  163 MET cc_start: 0.7935 (mtp) cc_final: 0.7688 (mtp)
REVERT: B  168 ARG cc_start: 0.8586 (ttp-170) cc_final: 0.8382 (ttp-170)
REVERT: B  266 LEU cc_start: 0.8702 (mt) cc_final: 0.8472 (mt)
REVERT: B  273 LEU cc_start: 0.8532 (mt) cc_final: 0.8275 (mp)
REVERT: B  316 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7059 (mt-10)
REVERT: B  340 THR cc_start: 0.8239 (m) cc_final: 0.7847 (p)
REVERT: B  435 VAL cc_start: 0.8597 (m) cc_final: 0.8342 (p)
  outliers start: 33
  outliers final: 24
  residues processed: 219
  average time/residue: 0.1144
  time to fit residues: 32.2825
Evaluate side-chains
  225 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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  228 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  324 ARG
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  228 VAL
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  485 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0470
   chunk 78 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0980
   chunk 69 optimal weight:    0.1980
   chunk 38 optimal weight:    0.5980
   chunk 41 optimal weight:    0.2980
   chunk 5 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.2278

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3913 r_free = 0.3913 target = 0.150853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130583 restraints weight = 10606.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.19
r_work: 0.3512 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7918  Z= 0.112
  Angle     :  0.541   8.216  10760  Z= 0.266
  Chirality :  0.041   0.149   1208
  Planarity :  0.005   0.041   1402
  Dihedral  :  5.700  57.581   1102
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 28.45 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.27), residues: 972
  helix:  1.87 (0.26), residues: 408
  sheet:  0.43 (0.38), residues: 160
  loop : -0.46 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 324 
 TYR   0.009   0.001   TYR B 172 
 PHE   0.010   0.001   PHE B  34 
 TRP   0.007   0.001   TRP A 391 
 HIS   0.009   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7916)
  covalent geometry    : angle       0.54087 (10760)
  hydrogen bonds       : bond        0.02911 (  393)
  hydrogen bonds       : angle       4.45432 ( 1095)
  Misc. bond           : bond        0.00031 (    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
  229 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 209
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8656 (m) cc_final: 0.8407 (t)
REVERT: A  154 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7018 (mt-10)
REVERT: A  163 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7866 (ttm)
REVERT: A  167 ASP cc_start: 0.8159 (m-30) cc_final: 0.7933 (m-30)
REVERT: A  304 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8205 (mt)
REVERT: A  319 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6867 (tm-30)
REVERT: A  324 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7087 (ttm170)
REVERT: B   94 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8088 (mp)
REVERT: B  139 MET cc_start: 0.7244 (mtm) cc_final: 0.6885 (mtm)
REVERT: B  158 ARG cc_start: 0.7582 (tpm170) cc_final: 0.7294 (tpm170)
REVERT: B  266 LEU cc_start: 0.8709 (mt) cc_final: 0.8485 (mt)
REVERT: B  273 LEU cc_start: 0.8510 (mt) cc_final: 0.8246 (mp)
REVERT: B  340 THR cc_start: 0.8209 (m) cc_final: 0.7835 (p)
  outliers start: 20
  outliers final: 13
  residues processed: 217
  average time/residue: 0.1165
  time to fit residues: 32.3733
Evaluate side-chains
  215 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 198
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
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  106 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  435 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  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0370
   chunk 76 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0770
   overall best weight:    0.4416

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.149351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.128994 restraints weight = 10623.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.21
r_work: 0.3489 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2270

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= 0.162
  Angle     :  0.589   9.985  10760  Z= 0.288
  Chirality :  0.043   0.149   1208
  Planarity :  0.005   0.043   1402
  Dihedral  :  5.725  55.536   1102
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 28.21 %
    Favored  : 69.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.27), residues: 972
  helix:  1.88 (0.26), residues: 408
  sheet:  0.40 (0.39), residues: 160
  loop : -0.40 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 168 
 TYR   0.009   0.001   TYR B 172 
 PHE   0.011   0.002   PHE B 199 
 TRP   0.011   0.001   TRP A 391 
 HIS   0.015   0.002   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 7916)
  covalent geometry    : angle       0.58946 (10760)
  hydrogen bonds       : bond        0.03105 (  393)
  hydrogen bonds       : angle       4.53779 ( 1095)
  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
  221 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLN cc_start: 0.7627 (mp10) cc_final: 0.7328 (mt0)
REVERT: A   96 SER cc_start: 0.8697 (m) cc_final: 0.8418 (t)
REVERT: A  154 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7031 (mt-10)
REVERT: A  163 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7859 (ttm)
REVERT: A  304 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8239 (mt)
REVERT: A  319 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6898 (tm-30)
REVERT: A  324 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6966 (ttm170)
REVERT: B   94 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8092 (mp)
REVERT: B  139 MET cc_start: 0.7236 (mtm) cc_final: 0.6940 (mtm)
REVERT: B  158 ARG cc_start: 0.7617 (tpm170) cc_final: 0.7355 (tpm170)
REVERT: B  266 LEU cc_start: 0.8707 (mt) cc_final: 0.8482 (mt)
REVERT: B  273 LEU cc_start: 0.8518 (mt) cc_final: 0.8256 (mp)
REVERT: B  340 THR cc_start: 0.8229 (m) cc_final: 0.7855 (p)
REVERT: B  435 VAL cc_start: 0.8579 (m) cc_final: 0.8325 (p)
  outliers start: 23
  outliers final: 17
  residues processed: 207
  average time/residue: 0.1179
  time to fit residues: 31.3011
Evaluate side-chains
  218 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  106 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 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  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  425 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0980
   chunk 44 optimal weight:    0.8980
   chunk 43 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 37 optimal weight:    0.4980
   chunk 96 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0870
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.3758

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.149568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.129232 restraints weight = 10616.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.19
r_work: 0.3498 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7918  Z= 0.148
  Angle     :  0.585   9.537  10760  Z= 0.286
  Chirality :  0.042   0.153   1208
  Planarity :  0.005   0.044   1402
  Dihedral  :  5.738  55.819   1102
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 28.33 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.27), residues: 972
  helix:  1.91 (0.26), residues: 408
  sheet:  0.43 (0.39), residues: 160
  loop : -0.42 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 168 
 TYR   0.009   0.001   TYR B 172 
 PHE   0.010   0.001   PHE A  34 
 TRP   0.011   0.001   TRP A 391 
 HIS   0.018   0.002   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7916)
  covalent geometry    : angle       0.58497 (10760)
  hydrogen bonds       : bond        0.03036 (  393)
  hydrogen bonds       : angle       4.51961 ( 1095)
  Misc. bond           : bond        0.00031 (    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
  223 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 198
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8689 (m) cc_final: 0.8416 (t)
REVERT: A  154 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7059 (mt-10)
REVERT: A  163 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7859 (ttm)
REVERT: A  167 ASP cc_start: 0.8178 (m-30) cc_final: 0.7955 (m-30)
REVERT: A  304 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8252 (mt)
REVERT: A  319 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6898 (tm-30)
REVERT: A  324 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6872 (ttm170)
REVERT: B   94 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8082 (mp)
REVERT: B  139 MET cc_start: 0.7235 (mtm) cc_final: 0.6898 (mtm)
REVERT: B  158 ARG cc_start: 0.7607 (tpm170) cc_final: 0.7331 (tpm170)
REVERT: B  266 LEU cc_start: 0.8709 (mt) cc_final: 0.8486 (mt)
REVERT: B  273 LEU cc_start: 0.8517 (mt) cc_final: 0.8249 (mp)
REVERT: B  340 THR cc_start: 0.8192 (m) cc_final: 0.7823 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 209
  average time/residue: 0.1116
  time to fit residues: 30.0467
Evaluate side-chains
  221 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 199
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  106 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   65 THR
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  183 ILE
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  425 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0770
   chunk 82 optimal weight:    0.1980
   chunk 40 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0970
   chunk 62 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3895 r_free = 0.3895 target = 0.149652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129326 restraints weight = 10575.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.19
r_work: 0.3505 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7918  Z= 0.137
  Angle     :  0.576   9.499  10760  Z= 0.282
  Chirality :  0.042   0.158   1208
  Planarity :  0.005   0.041   1402
  Dihedral  :  5.722  56.278   1102
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 28.10 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.27), residues: 972
  helix:  1.94 (0.26), residues: 408
  sheet:  0.29 (0.38), residues: 170
  loop : -0.35 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 168 
 TYR   0.009   0.001   TYR B 172 
 PHE   0.010   0.001   PHE B  34 
 TRP   0.011   0.001   TRP A 391 
 HIS   0.019   0.002   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7916)
  covalent geometry    : angle       0.57574 (10760)
  hydrogen bonds       : bond        0.02989 (  393)
  hydrogen bonds       : angle       4.48458 ( 1095)
  Misc. bond           : bond        0.00031 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2739.50 seconds
wall clock time: 47 minutes 30.94 seconds (2850.94 seconds total)