Starting phenix.real_space_refine
on Wed Mar  4 05:18:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lgm_23327/03_2026/7lgm_23327.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lgm_23327/03_2026/7lgm_23327.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lgm_23327/03_2026/7lgm_23327.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lgm_23327/03_2026/7lgm_23327.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lgm_23327/03_2026/7lgm_23327.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lgm_23327/03_2026/7lgm_23327.cif"
  }
  resolution = 4.4
  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=   0.053
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      46      5.16       5
     C    6842      2.51       5
     N    1942      2.21       5
     O    2118      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10954
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 719, 5446
          Classifications: {'peptide': 719}
          Link IDs: {'PTRANS': 25, 'TRANS': 693}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.28, per 1000 atoms: 0.39
  Number of scatterers: 10954
  At special positions: 0
  Unit cell: (121.8, 138.04, 97.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     P       6     15.00
     O    2118      8.00
     N    1942      7.00
     C    6842      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 511.8 milliseconds
  

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2608

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 14 sheets defined
      37.7% alpha, 14.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
      removed outlier: 4.605A  pdb=" N   VAL A  14 " --> pdb=" O   GLY A  11 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   TYR A  15 " --> pdb=" O   PRO A  12 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 11 through 15'
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 40 through 50
      removed outlier: 3.566A  pdb=" N   LYS A  48 " --> pdb=" O   GLU A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 75 through 84
    Processing helix  chain 'A' and resid 85 through 91
    Processing helix  chain 'A' and resid 121 through 136
    Processing helix  chain 'A' and resid 145 through 160
      removed outlier: 3.653A  pdb=" N   ASP A 149 " --> pdb=" O   ASP A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 175
      removed outlier: 4.135A  pdb=" N   LEU A 169 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 218
    Processing helix  chain 'A' and resid 218 through 228
    Processing helix  chain 'A' and resid 246 through 251
    Processing helix  chain 'A' and resid 275 through 287
      removed outlier: 4.010A  pdb=" N   ASP A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE A 285 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 340
    Processing helix  chain 'A' and resid 359 through 369
    Processing helix  chain 'A' and resid 405 through 420
    Processing helix  chain 'A' and resid 436 through 440
    Processing helix  chain 'A' and resid 452 through 456
      removed outlier: 3.506A  pdb=" N   MET A 455 " --> pdb=" O   GLY A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 473
    Processing helix  chain 'A' and resid 497 through 510
    Processing helix  chain 'A' and resid 535 through 544
    Processing helix  chain 'A' and resid 556 through 564
    Processing helix  chain 'A' and resid 593 through 603
      removed outlier: 3.879A  pdb=" N   VAL A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   ILE A 601 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 624
    Processing helix  chain 'A' and resid 645 through 649
    Processing helix  chain 'A' and resid 679 through 685
      Proline residue:  A 682  - end of helix
    Processing helix  chain 'A' and resid 692 through 706
    Processing helix  chain 'A' and resid 710 through 719
    Processing helix  chain 'B' and resid 11 through 15
      removed outlier: 4.606A  pdb=" N   VAL B  14 " --> pdb=" O   GLY B  11 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   TYR B  15 " --> pdb=" O   PRO B  12 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 11 through 15'
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'B' and resid 40 through 50
      removed outlier: 3.567A  pdb=" N   LYS B  48 " --> pdb=" O   GLU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 69
    Processing helix  chain 'B' and resid 75 through 84
    Processing helix  chain 'B' and resid 85 through 91
    Processing helix  chain 'B' and resid 121 through 136
    Processing helix  chain 'B' and resid 145 through 160
      removed outlier: 3.654A  pdb=" N   ASP B 149 " --> pdb=" O   ASP B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 175
      removed outlier: 4.135A  pdb=" N   LEU B 169 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 218
    Processing helix  chain 'B' and resid 218 through 228
    Processing helix  chain 'B' and resid 246 through 251
    Processing helix  chain 'B' and resid 275 through 287
      removed outlier: 4.010A  pdb=" N   ASP B 284 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 340
    Processing helix  chain 'B' and resid 359 through 369
    Processing helix  chain 'B' and resid 405 through 420
    Processing helix  chain 'B' and resid 436 through 440
    Processing helix  chain 'B' and resid 452 through 456
      removed outlier: 3.505A  pdb=" N   MET B 455 " --> pdb=" O   GLY B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 473
    Processing helix  chain 'B' and resid 497 through 510
    Processing helix  chain 'B' and resid 535 through 544
    Processing helix  chain 'B' and resid 556 through 564
    Processing helix  chain 'B' and resid 593 through 603
      removed outlier: 3.879A  pdb=" N   VAL B 600 " --> pdb=" O   GLU B 596 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   ILE B 601 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 624
    Processing helix  chain 'B' and resid 645 through 649
    Processing helix  chain 'B' and resid 679 through 685
      Proline residue:  B 682  - end of helix
    Processing helix  chain 'B' and resid 692 through 706
    Processing helix  chain 'B' and resid 710 through 719
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 9
      removed outlier: 5.649A  pdb=" N   ILE A   3 " --> pdb=" O   VAL A  24 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   VAL A  24 " --> pdb=" O   ILE A   3 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   LEU A 111 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ALA A  98 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   SER A 113 " --> pdb=" O   GLY A  96 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 182
    Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 273
      removed outlier: 6.189A  pdb=" N   VAL A 256 " --> pdb=" O   ASN A 272 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 318
      removed outlier: 7.001A  pdb=" N   LEU A 307 " --> pdb=" O   VAL A 314 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ALA A 316 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ARG A 305 " --> pdb=" O   ALA A 316 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ARG A 318 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   ASP A 303 " --> pdb=" O   ARG A 318 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ASP A 427 " --> pdb=" O   CYS A 445 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 325
    Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 527
      removed outlier: 7.860A  pdb=" N   GLY A 514 " --> pdb=" O   VAL A 552 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ILE A 486 " --> pdb=" O   ALA A 551 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   LEU A 553 " --> pdb=" O   ILE A 486 " (cutoff:3.500A)
      removed outlier: 9.642A  pdb=" N   ALA A 488 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   ALA A 487 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   ALA A 574 " --> pdb=" O   ALA A 487 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   ILE A 489 " --> pdb=" O   ALA A 574 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   ASP A 571 " --> pdb=" O   LYS A 606 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 632 through 634
      removed outlier: 6.292A  pdb=" N   TYR A 632 " --> pdb=" O   VAL A 653 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   LEU A 655 " --> pdb=" O   TYR A 632 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   THR A 634 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
      removed outlier: 9.245A  pdb=" N   LYS A 657 " --> pdb=" O   THR A 634 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ASP A 662 " --> pdb=" O   TRP A 677 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   TRP A 677 " --> pdb=" O   ASP A 662 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ILE A 664 " --> pdb=" O   LEU A 675 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 9
      removed outlier: 5.648A  pdb=" N   ILE B   3 " --> pdb=" O   VAL B  24 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   VAL B  24 " --> pdb=" O   ILE B   3 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LEU B 111 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ALA B  98 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   SER B 113 " --> pdb=" O   GLY B  96 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 182
    Processing sheet with id=AB1, first strand: chain 'B' and resid 270 through 273
      removed outlier: 6.190A  pdb=" N   VAL B 256 " --> pdb=" O   ASN B 272 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 318
      removed outlier: 7.001A  pdb=" N   LEU B 307 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ALA B 316 " --> pdb=" O   ARG B 305 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ARG B 305 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ARG B 318 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 318 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ASP B 427 " --> pdb=" O   CYS B 445 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 323 through 325
    Processing sheet with id=AB4, first strand: chain 'B' and resid 526 through 527
      removed outlier: 7.861A  pdb=" N   GLY B 514 " --> pdb=" O   VAL B 552 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ILE B 486 " --> pdb=" O   ALA B 551 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   LEU B 553 " --> pdb=" O   ILE B 486 " (cutoff:3.500A)
      removed outlier: 9.642A  pdb=" N   ALA B 488 " --> pdb=" O   LEU B 553 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   ALA B 487 " --> pdb=" O   VAL B 572 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   ALA B 574 " --> pdb=" O   ALA B 487 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   ILE B 489 " --> pdb=" O   ALA B 574 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   ASP B 571 " --> pdb=" O   LYS B 606 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 632 through 634
      removed outlier: 6.292A  pdb=" N   TYR B 632 " --> pdb=" O   VAL B 653 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   LEU B 655 " --> pdb=" O   TYR B 632 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   THR B 634 " --> pdb=" O   LEU B 655 " (cutoff:3.500A)
      removed outlier: 9.245A  pdb=" N   LYS B 657 " --> pdb=" O   THR B 634 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ASP B 662 " --> pdb=" O   TRP B 677 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   TRP B 677 " --> pdb=" O   ASP B 662 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   ILE B 664 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1128 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: 1.75

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1989
        1.31 -     1.44: 2642
        1.44 -     1.57: 6293
        1.57 -     1.70: 112
        1.70 -     1.83: 80
  Bond restraints: 11116
  Sorted by residual:
  bond pdb=" CB  HIS A 645 "
       pdb=" CG  HIS A 645 "
    ideal  model  delta    sigma   weight residual
    1.497  1.416  0.081 1.40e-02 5.10e+03 3.35e+01
  bond pdb=" CB  HIS B 645 "
       pdb=" CG  HIS B 645 "
    ideal  model  delta    sigma   weight residual
    1.497  1.417  0.080 1.40e-02 5.10e+03 3.28e+01
  bond pdb=" CB  TYR B 114 "
       pdb=" CG  TYR B 114 "
    ideal  model  delta    sigma   weight residual
    1.512  1.395  0.117 2.20e-02 2.07e+03 2.85e+01
  bond pdb=" CB  TYR A 114 "
       pdb=" CG  TYR A 114 "
    ideal  model  delta    sigma   weight residual
    1.512  1.395  0.117 2.20e-02 2.07e+03 2.80e+01
  bond pdb=" CB  LEU A 183 "
       pdb=" CG  LEU A 183 "
    ideal  model  delta    sigma   weight residual
    1.530  1.629 -0.099 2.00e-02 2.50e+03 2.43e+01
  ... (remaining 11111 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 13337
        2.80 -     5.61: 1524
        5.61 -     8.41: 202
        8.41 -    11.22: 17
       11.22 -    14.02: 2
  Bond angle restraints: 15082
  Sorted by residual:
  angle pdb=" N   LEU B 591 "
        pdb=" CA  LEU B 591 "
        pdb=" C   LEU B 591 "
      ideal   model   delta    sigma   weight residual
     113.88   99.86   14.02 1.23e+00 6.61e-01 1.30e+02
  angle pdb=" N   LEU A 591 "
        pdb=" CA  LEU A 591 "
        pdb=" C   LEU A 591 "
      ideal   model   delta    sigma   weight residual
     113.88   99.87   14.01 1.23e+00 6.61e-01 1.30e+02
  angle pdb=" CA  ASP A 662 "
        pdb=" CB  ASP A 662 "
        pdb=" CG  ASP A 662 "
      ideal   model   delta    sigma   weight residual
     112.60  121.57   -8.97 1.00e+00 1.00e+00 8.04e+01
  angle pdb=" CA  ASP B 662 "
        pdb=" CB  ASP B 662 "
        pdb=" CG  ASP B 662 "
      ideal   model   delta    sigma   weight residual
     112.60  121.51   -8.91 1.00e+00 1.00e+00 7.94e+01
  angle pdb=" N   THR A  52 "
        pdb=" CA  THR A  52 "
        pdb=" C   THR A  52 "
      ideal   model   delta    sigma   weight residual
     114.56  104.13   10.43 1.27e+00 6.20e-01 6.75e+01
  ... (remaining 15077 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 6485
       17.54 -    35.08: 214
       35.08 -    52.62: 49
       52.62 -    70.16: 26
       70.16 -    87.70: 4
  Dihedral angle restraints: 6778
    sinusoidal: 2694
      harmonic: 4084
  Sorted by residual:
  dihedral pdb=" C   TRP A 677 "
           pdb=" N   TRP A 677 "
           pdb=" CA  TRP A 677 "
           pdb=" CB  TRP A 677 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.60   -9.00     0      2.50e+00 1.60e-01 1.30e+01
  dihedral pdb=" N   PHE B 254 "
           pdb=" C   PHE B 254 "
           pdb=" CA  PHE B 254 "
           pdb=" CB  PHE B 254 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.80   -9.00     0      2.50e+00 1.60e-01 1.30e+01
  dihedral pdb=" C   TRP B 677 "
           pdb=" N   TRP B 677 "
           pdb=" CA  TRP B 677 "
           pdb=" CB  TRP B 677 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.61   -8.99     0      2.50e+00 1.60e-01 1.29e+01
  ... (remaining 6775 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 1197
       0.097 -    0.193: 465
       0.193 -    0.290: 96
       0.290 -    0.387: 8
       0.387 -    0.484: 2
  Chirality restraints: 1768
  Sorted by residual:
  chirality pdb=" CA  PHE A 254 "
            pdb=" N   PHE A 254 "
            pdb=" C   PHE A 254 "
            pdb=" CB  PHE A 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.85e+00
  chirality pdb=" CA  PHE B 254 "
            pdb=" N   PHE B 254 "
            pdb=" C   PHE B 254 "
            pdb=" CB  PHE B 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.82e+00
  chirality pdb=" CA  SER A 209 "
            pdb=" N   SER A 209 "
            pdb=" C   SER A 209 "
            pdb=" CB  SER A 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.51e+00
  ... (remaining 1765 not shown)

  Planarity restraints: 1964
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 196 "    0.055 2.00e-02 2.50e+03   2.92e-02 1.71e+01
        pdb=" CG  TYR A 196 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 196 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 196 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 196 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 196 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 196 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 196 "    0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 196 "   -0.055 2.00e-02 2.50e+03   2.91e-02 1.70e+01
        pdb=" CG  TYR B 196 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 196 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 196 "    0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 196 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 196 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 196 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 196 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  31 "    0.047 2.00e-02 2.50e+03   2.67e-02 1.42e+01
        pdb=" CG  TYR A  31 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  31 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  31 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  31 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  31 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  31 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A  31 "    0.040 2.00e-02 2.50e+03
  ... (remaining 1961 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 4442
        2.90 -     3.40: 10910
        3.40 -     3.90: 18562
        3.90 -     4.40: 22124
        4.40 -     4.90: 34208
  Nonbonded interactions: 90246
  Sorted by model distance:
  nonbonded pdb=" N   LEU B 591 "
            pdb=" N   ASP B 592 "
     model   vdw
     2.398 2.560
  nonbonded pdb=" N   LEU A 591 "
            pdb=" N   ASP A 592 "
     model   vdw
     2.398 2.560
  nonbonded pdb=" N   ASP A 145 "
            pdb=" OD1 ASP A 145 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" N   ASP B 145 "
            pdb=" OD1 ASP B 145 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" N   THR B  52 "
            pdb=" N   LEU B  53 "
     model   vdw
     2.439 2.560
  ... (remaining 90241 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: 0.02
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 group one per residue
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:             2.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.790
  Find NCS groups from input model:        0.080
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5343
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      :  0.018   0.117  11116  Z= 0.982
  Angle     :  1.880  14.020  15082  Z= 1.274
  Chirality :  0.101   0.484   1768
  Planarity :  0.009   0.031   1964
  Dihedral  : 10.723  87.702   4170
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.21), residues: 1434
  helix: -1.40 (0.20), residues: 468
  sheet:  0.55 (0.44), residues: 148
  loop : -1.03 (0.21), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 438 
 TYR   0.055   0.010   TYR A 196 
 PHE   0.015   0.006   PHE A 153 
 TRP   0.017   0.006   TRP A 180 
 HIS   0.007   0.002   HIS B 679 

Details of bonding type rmsd
  covalent geometry    : bond        0.01807 (11116)
  covalent geometry    : angle       1.88043 (15082)
  hydrogen bonds       : bond        0.19667 (  424)
  hydrogen bonds       : angle       7.92669 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  417 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 417
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.8612 (mt) cc_final: 0.7663 (mt)
REVERT: A  219 LYS cc_start: 0.5665 (pttm) cc_final: 0.5447 (pttt)
REVERT: A  220 ASN cc_start: 0.8047 (m-40) cc_final: 0.7675 (m-40)
REVERT: A  303 ASP cc_start: 0.8251 (m-30) cc_final: 0.7828 (t0)
REVERT: A  336 ILE cc_start: 0.7906 (mm) cc_final: 0.7660 (mm)
REVERT: A  386 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7364 (mmm-85)
REVERT: A  448 ASN cc_start: 0.5545 (t0) cc_final: 0.4761 (t0)
REVERT: A  508 MET cc_start: 0.6755 (mmp) cc_final: 0.6046 (mtp)
REVERT: A  521 VAL cc_start: 0.9024 (t) cc_final: 0.8817 (m)
REVERT: A  645 HIS cc_start: 0.7097 (t70) cc_final: 0.6788 (t70)
REVERT: A  697 MET cc_start: 0.5429 (mtp) cc_final: 0.5200 (mtp)
REVERT: B   21 ILE cc_start: 0.8600 (mt) cc_final: 0.7604 (mt)
REVERT: B  220 ASN cc_start: 0.8141 (m-40) cc_final: 0.7685 (m-40)
REVERT: B  303 ASP cc_start: 0.8182 (m-30) cc_final: 0.7754 (t0)
REVERT: B  336 ILE cc_start: 0.7699 (mm) cc_final: 0.7329 (mm)
REVERT: B  386 ARG cc_start: 0.7882 (mmt-90) cc_final: 0.7502 (mmm-85)
REVERT: B  421 LEU cc_start: 0.8833 (mt) cc_final: 0.8589 (mt)
REVERT: B  476 PHE cc_start: 0.8317 (m-80) cc_final: 0.8076 (m-80)
REVERT: B  508 MET cc_start: 0.6708 (mmp) cc_final: 0.6387 (mtp)
REVERT: B  521 VAL cc_start: 0.8982 (t) cc_final: 0.8615 (m)
REVERT: B  645 HIS cc_start: 0.7025 (t70) cc_final: 0.6692 (t70)
REVERT: B  695 ASN cc_start: 0.8509 (m-40) cc_final: 0.8307 (m110)
REVERT: B  697 MET cc_start: 0.5703 (mtp) cc_final: 0.5262 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 417
  average time/residue: 0.1201
  time to fit residues: 67.7859
Evaluate side-chains
  245 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  86 HIS
A 224 GLN
A 304 HIS
A 448 ASN
A 481 GLN
A 679 HIS
** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  86 HIS
B 224 GLN
B 304 HIS
B 679 HIS
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.183824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.155455 restraints weight = 27795.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.158874 restraints weight = 18934.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.161358 restraints weight = 14168.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.162884 restraints weight = 11407.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.164302 restraints weight = 9807.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6348
moved from start:          0.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11116  Z= 0.189
  Angle     :  0.799   9.193  15082  Z= 0.427
  Chirality :  0.049   0.248   1768
  Planarity :  0.005   0.072   1964
  Dihedral  :  7.318  57.938   1620
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  3.28 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.21), residues: 1434
  helix:  0.07 (0.23), residues: 472
  sheet: -0.23 (0.42), residues: 166
  loop : -1.34 (0.22), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 305 
 TYR   0.013   0.002   TYR B 704 
 PHE   0.018   0.003   PHE B 153 
 TRP   0.012   0.002   TRP B 677 
 HIS   0.008   0.001   HIS B 645 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (11116)
  covalent geometry    : angle       0.79945 (15082)
  hydrogen bonds       : bond        0.04607 (  424)
  hydrogen bonds       : angle       6.32229 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 309
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8737 (mt) cc_final: 0.7855 (mt)
REVERT: A  170 VAL cc_start: 0.8771 (t) cc_final: 0.8275 (p)
REVERT: A  336 ILE cc_start: 0.7993 (mm) cc_final: 0.7773 (mm)
REVERT: A  352 MET cc_start: 0.5924 (ptp) cc_final: 0.5659 (ptp)
REVERT: A  404 ILE cc_start: 0.5120 (mm) cc_final: 0.4538 (tt)
REVERT: A  409 LYS cc_start: 0.7170 (mtmt) cc_final: 0.6707 (mtpt)
REVERT: A  428 PHE cc_start: 0.7565 (t80) cc_final: 0.7098 (t80)
REVERT: A  430 THR cc_start: 0.8793 (t) cc_final: 0.8587 (m)
REVERT: A  508 MET cc_start: 0.6852 (mmp) cc_final: 0.6191 (mtt)
REVERT: A  555 THR cc_start: 0.8002 (t) cc_final: 0.7679 (t)
REVERT: A  577 ASN cc_start: 0.7928 (t0) cc_final: 0.7412 (p0)
REVERT: A  695 ASN cc_start: 0.8937 (m-40) cc_final: 0.8665 (m110)
REVERT: B  170 VAL cc_start: 0.8799 (t) cc_final: 0.8301 (p)
REVERT: B  336 ILE cc_start: 0.8053 (mm) cc_final: 0.7800 (mm)
REVERT: B  385 LEU cc_start: 0.7885 (mm) cc_final: 0.7146 (tp)
REVERT: B  386 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.6220 (mtt180)
REVERT: B  404 ILE cc_start: 0.5206 (mm) cc_final: 0.4800 (tt)
REVERT: B  409 LYS cc_start: 0.7065 (mtmt) cc_final: 0.6563 (mtpt)
REVERT: B  428 PHE cc_start: 0.7427 (t80) cc_final: 0.7056 (t80)
REVERT: B  508 MET cc_start: 0.6923 (mmp) cc_final: 0.6344 (mtt)
REVERT: B  555 THR cc_start: 0.8233 (t) cc_final: 0.8001 (p)
REVERT: B  570 CYS cc_start: 0.8555 (p) cc_final: 0.8312 (p)
REVERT: B  577 ASN cc_start: 0.7939 (t0) cc_final: 0.7374 (p0)
REVERT: B  692 ASN cc_start: 0.6744 (m-40) cc_final: 0.6273 (t0)
REVERT: B  695 ASN cc_start: 0.8998 (m-40) cc_final: 0.8742 (m110)
  outliers start: 2
  outliers final: 2
  residues processed: 311
  average time/residue: 0.1114
  time to fit residues: 48.3817
Evaluate side-chains
  203 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 201
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 5 optimal weight:    0.0670
   chunk 83 optimal weight:    2.9990
   chunk 127 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 92 optimal weight:    0.5980
   chunk 137 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   chunk 112 optimal weight:    0.7980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 448 ASN
A 481 GLN
A 679 HIS
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 GLN
B 679 HIS
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.178135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.149388 restraints weight = 25045.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.153008 restraints weight = 16398.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.155569 restraints weight = 11882.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.157358 restraints weight = 9343.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.158649 restraints weight = 7856.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6382
moved from start:          0.5703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11116  Z= 0.151
  Angle     :  0.722   6.603  15082  Z= 0.385
  Chirality :  0.048   0.366   1768
  Planarity :  0.005   0.078   1964
  Dihedral  :  6.920  46.294   1620
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.93 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.21), residues: 1434
  helix:  0.08 (0.23), residues: 480
  sheet: -0.74 (0.39), residues: 174
  loop : -1.53 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 305 
 TYR   0.022   0.001   TYR B 156 
 PHE   0.028   0.003   PHE A 698 
 TRP   0.016   0.002   TRP B 677 
 HIS   0.004   0.001   HIS B  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (11116)
  covalent geometry    : angle       0.72187 (15082)
  hydrogen bonds       : bond        0.04111 (  424)
  hydrogen bonds       : angle       6.06619 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 269
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 ASN cc_start: 0.8454 (m-40) cc_final: 0.7498 (m-40)
REVERT: A  336 ILE cc_start: 0.8000 (mm) cc_final: 0.7716 (mm)
REVERT: A  352 MET cc_start: 0.6395 (ptp) cc_final: 0.5775 (ptt)
REVERT: A  355 LYS cc_start: 0.7489 (tppt) cc_final: 0.6927 (ptmt)
REVERT: A  385 LEU cc_start: 0.7529 (mm) cc_final: 0.7049 (tt)
REVERT: A  386 ARG cc_start: 0.7791 (mmt-90) cc_final: 0.6081 (mtt90)
REVERT: A  492 THR cc_start: 0.6236 (p) cc_final: 0.5945 (p)
REVERT: A  508 MET cc_start: 0.6990 (mmp) cc_final: 0.6554 (mtp)
REVERT: A  692 ASN cc_start: 0.6407 (t0) cc_final: 0.5760 (t0)
REVERT: A  697 MET cc_start: 0.7808 (mtm) cc_final: 0.7513 (mtp)
REVERT: B  119 ILE cc_start: 0.6603 (pt) cc_final: 0.6125 (pt)
REVERT: B  220 ASN cc_start: 0.8610 (m-40) cc_final: 0.7659 (m-40)
REVERT: B  336 ILE cc_start: 0.7992 (mm) cc_final: 0.7726 (mm)
REVERT: B  352 MET cc_start: 0.6162 (ptp) cc_final: 0.5787 (ptt)
REVERT: B  355 LYS cc_start: 0.7440 (mmmt) cc_final: 0.6627 (ptpt)
REVERT: B  385 LEU cc_start: 0.7650 (mm) cc_final: 0.7103 (tt)
REVERT: B  386 ARG cc_start: 0.7679 (mmt-90) cc_final: 0.5664 (mtt180)
REVERT: B  409 LYS cc_start: 0.7097 (mtmt) cc_final: 0.6589 (mtpt)
REVERT: B  508 MET cc_start: 0.7132 (mmp) cc_final: 0.6865 (mtp)
REVERT: B  570 CYS cc_start: 0.8556 (p) cc_final: 0.8327 (p)
REVERT: B  577 ASN cc_start: 0.8083 (t0) cc_final: 0.7750 (p0)
REVERT: B  692 ASN cc_start: 0.6852 (m-40) cc_final: 0.6427 (t0)
REVERT: B  695 ASN cc_start: 0.8959 (m-40) cc_final: 0.8742 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 269
  average time/residue: 0.1276
  time to fit residues: 46.6045
Evaluate side-chains
  185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0670
   chunk 64 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 131 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    0.9324

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 GLN
A 645 HIS
B 143 GLN
** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 629 HIS
B 645 HIS
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 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 = 0.4393 r_free = 0.4393 target = 0.170871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.140423 restraints weight = 25679.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.143611 restraints weight = 17331.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.145864 restraints weight = 12936.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.147203 restraints weight = 10451.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.148558 restraints weight = 9079.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6671
moved from start:          0.6963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11116  Z= 0.166
  Angle     :  0.720   8.342  15082  Z= 0.382
  Chirality :  0.047   0.283   1768
  Planarity :  0.005   0.077   1964
  Dihedral  :  7.354  53.602   1620
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.51 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.21), residues: 1434
  helix:  0.13 (0.23), residues: 480
  sheet: -0.63 (0.40), residues: 168
  loop : -1.77 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 251 
 TYR   0.018   0.002   TYR B 156 
 PHE   0.021   0.003   PHE A 153 
 TRP   0.010   0.002   TRP A 677 
 HIS   0.010   0.002   HIS B 645 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (11116)
  covalent geometry    : angle       0.72021 (15082)
  hydrogen bonds       : bond        0.03885 (  424)
  hydrogen bonds       : angle       5.93475 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8123 (mtm180)
REVERT: A  170 VAL cc_start: 0.8787 (t) cc_final: 0.8375 (p)
REVERT: A  220 ASN cc_start: 0.8608 (m-40) cc_final: 0.7975 (m-40)
REVERT: A  336 ILE cc_start: 0.8081 (mm) cc_final: 0.7810 (mm)
REVERT: A  352 MET cc_start: 0.6260 (ptp) cc_final: 0.5866 (ptt)
REVERT: A  355 LYS cc_start: 0.7633 (tppt) cc_final: 0.6890 (ptmt)
REVERT: A  409 LYS cc_start: 0.7712 (mtmt) cc_final: 0.7168 (ptmt)
REVERT: A  501 MET cc_start: 0.7822 (mmm) cc_final: 0.7319 (mmm)
REVERT: A  621 MET cc_start: 0.6619 (mmm) cc_final: 0.6236 (mmm)
REVERT: A  644 GLU cc_start: 0.7650 (pp20) cc_final: 0.7348 (mp0)
REVERT: A  692 ASN cc_start: 0.6869 (t0) cc_final: 0.6125 (t0)
REVERT: B   89 ARG cc_start: 0.8774 (mtp180) cc_final: 0.8063 (mtm180)
REVERT: B  119 ILE cc_start: 0.6648 (pt) cc_final: 0.6288 (pt)
REVERT: B  170 VAL cc_start: 0.8794 (t) cc_final: 0.8416 (p)
REVERT: B  220 ASN cc_start: 0.8545 (m-40) cc_final: 0.7766 (m-40)
REVERT: B  336 ILE cc_start: 0.8067 (mm) cc_final: 0.7815 (mm)
REVERT: B  352 MET cc_start: 0.6080 (ptp) cc_final: 0.5776 (ptt)
REVERT: B  492 THR cc_start: 0.6191 (p) cc_final: 0.5989 (p)
REVERT: B  644 GLU cc_start: 0.7737 (pp20) cc_final: 0.7408 (mp0)
REVERT: B  692 ASN cc_start: 0.6950 (m-40) cc_final: 0.6598 (t0)
REVERT: B  695 ASN cc_start: 0.8904 (m-40) cc_final: 0.8622 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1164
  time to fit residues: 38.4999
Evaluate side-chains
  189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 93 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 129 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 125 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN
B 177 ASN
** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 GLN
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.169611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.138396 restraints weight = 25290.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.141770 restraints weight = 16727.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.144140 restraints weight = 12306.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.145824 restraints weight = 9859.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.146998 restraints weight = 8401.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.7592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11116  Z= 0.160
  Angle     :  0.709   8.220  15082  Z= 0.375
  Chirality :  0.047   0.219   1768
  Planarity :  0.005   0.073   1964
  Dihedral  :  7.229  53.586   1620
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.14 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.41 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.21), residues: 1434
  helix:  0.17 (0.23), residues: 482
  sheet: -0.46 (0.42), residues: 158
  loop : -1.78 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 483 
 TYR   0.015   0.002   TYR B 156 
 PHE   0.024   0.003   PHE B 698 
 TRP   0.005   0.001   TRP A 677 
 HIS   0.005   0.001   HIS B 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (11116)
  covalent geometry    : angle       0.70899 (15082)
  hydrogen bonds       : bond        0.03819 (  424)
  hydrogen bonds       : angle       5.78576 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 229
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 VAL cc_start: 0.8770 (t) cc_final: 0.8383 (p)
REVERT: A  220 ASN cc_start: 0.8305 (m-40) cc_final: 0.8048 (m-40)
REVERT: A  336 ILE cc_start: 0.8196 (mm) cc_final: 0.7949 (mm)
REVERT: A  352 MET cc_start: 0.6347 (ptp) cc_final: 0.5942 (ptt)
REVERT: A  386 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.6269 (mtt180)
REVERT: A  409 LYS cc_start: 0.7614 (mtmt) cc_final: 0.7056 (ptmt)
REVERT: A  501 MET cc_start: 0.8010 (mmm) cc_final: 0.7729 (mmm)
REVERT: A  621 MET cc_start: 0.6635 (mmm) cc_final: 0.5583 (mtt)
REVERT: A  692 ASN cc_start: 0.6924 (t0) cc_final: 0.6149 (t0)
REVERT: B   53 LEU cc_start: 0.8777 (mt) cc_final: 0.8528 (mt)
REVERT: B  170 VAL cc_start: 0.8769 (t) cc_final: 0.8347 (p)
REVERT: B  220 ASN cc_start: 0.8319 (m-40) cc_final: 0.7752 (m-40)
REVERT: B  336 ILE cc_start: 0.8071 (mm) cc_final: 0.7835 (mm)
REVERT: B  352 MET cc_start: 0.6021 (ptp) cc_final: 0.5789 (ptt)
REVERT: B  492 THR cc_start: 0.6509 (p) cc_final: 0.6271 (p)
REVERT: B  692 ASN cc_start: 0.7060 (m-40) cc_final: 0.6827 (t0)
REVERT: B  695 ASN cc_start: 0.8899 (m-40) cc_final: 0.8667 (m110)
  outliers start: 1
  outliers final: 1
  residues processed: 230
  average time/residue: 0.1132
  time to fit residues: 36.4103
Evaluate side-chains
  185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 115 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9990
   chunk 138 optimal weight:    0.0040
   chunk 94 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0970
   chunk 11 optimal weight:    0.8980
   chunk 107 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 GLN
** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 GLN
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 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 = 0.4396 r_free = 0.4396 target = 0.171669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.141124 restraints weight = 25150.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.144678 restraints weight = 16368.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.147099 restraints weight = 11932.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.148786 restraints weight = 9482.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.149993 restraints weight = 8045.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          0.7990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11116  Z= 0.132
  Angle     :  0.686  12.078  15082  Z= 0.358
  Chirality :  0.048   0.216   1768
  Planarity :  0.005   0.070   1964
  Dihedral  :  7.019  52.077   1620
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.16 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.22), residues: 1434
  helix:  0.34 (0.24), residues: 478
  sheet: -0.46 (0.40), residues: 158
  loop : -1.78 (0.21), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 483 
 TYR   0.014   0.001   TYR B 156 
 PHE   0.026   0.002   PHE B 698 
 TRP   0.005   0.001   TRP B 180 
 HIS   0.008   0.001   HIS B 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (11116)
  covalent geometry    : angle       0.68567 (15082)
  hydrogen bonds       : bond        0.03606 (  424)
  hydrogen bonds       : angle       5.65021 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.5960 (mmt) cc_final: 0.5690 (mmt)
REVERT: A  170 VAL cc_start: 0.8771 (t) cc_final: 0.8208 (p)
REVERT: A  336 ILE cc_start: 0.8207 (mm) cc_final: 0.7968 (mm)
REVERT: A  352 MET cc_start: 0.6459 (ptp) cc_final: 0.5991 (ptt)
REVERT: A  355 LYS cc_start: 0.7572 (tppt) cc_final: 0.6885 (ptmt)
REVERT: A  386 ARG cc_start: 0.8286 (mmt-90) cc_final: 0.7267 (mtt90)
REVERT: A  501 MET cc_start: 0.7997 (mmm) cc_final: 0.7579 (mmm)
REVERT: A  621 MET cc_start: 0.6566 (mmm) cc_final: 0.5726 (mtt)
REVERT: A  644 GLU cc_start: 0.7824 (pp20) cc_final: 0.7332 (mp0)
REVERT: A  677 TRP cc_start: 0.4974 (m-10) cc_final: 0.4587 (m-10)
REVERT: A  692 ASN cc_start: 0.7028 (t0) cc_final: 0.6322 (t0)
REVERT: A  697 MET cc_start: 0.7750 (mtt) cc_final: 0.7456 (mtt)
REVERT: B  220 ASN cc_start: 0.8378 (m-40) cc_final: 0.7923 (m-40)
REVERT: B  336 ILE cc_start: 0.8226 (mm) cc_final: 0.7984 (mm)
REVERT: B  355 LYS cc_start: 0.7546 (mmpt) cc_final: 0.7042 (ptpt)
REVERT: B  483 ARG cc_start: 0.7256 (mmt180) cc_final: 0.7014 (mmt180)
REVERT: B  603 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7503 (tp30)
REVERT: B  644 GLU cc_start: 0.7848 (pp20) cc_final: 0.7280 (mp0)
REVERT: B  677 TRP cc_start: 0.5025 (m-10) cc_final: 0.4720 (m-10)
REVERT: B  692 ASN cc_start: 0.7134 (m-40) cc_final: 0.6929 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1101
  time to fit residues: 36.7757
Evaluate side-chains
  188 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0980
   chunk 37 optimal weight:    0.0270
   chunk 82 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0980
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.2438

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.173725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.142937 restraints weight = 25193.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.146452 restraints weight = 16387.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.148874 restraints weight = 11956.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.150615 restraints weight = 9561.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.151822 restraints weight = 8122.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6615
moved from start:          0.8396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11116  Z= 0.125
  Angle     :  0.667   8.747  15082  Z= 0.349
  Chirality :  0.047   0.278   1768
  Planarity :  0.005   0.072   1964
  Dihedral  :  6.720  48.704   1620
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.86 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.22), residues: 1434
  helix:  0.36 (0.24), residues: 478
  sheet: -0.76 (0.37), residues: 182
  loop : -1.74 (0.22), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 483 
 TYR   0.012   0.001   TYR B 156 
 PHE   0.025   0.002   PHE B 698 
 TRP   0.006   0.001   TRP A 677 
 HIS   0.017   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (11116)
  covalent geometry    : angle       0.66656 (15082)
  hydrogen bonds       : bond        0.03583 (  424)
  hydrogen bonds       : angle       5.72355 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 ILE cc_start: 0.8190 (mm) cc_final: 0.7945 (mm)
REVERT: A  352 MET cc_start: 0.6180 (ptp) cc_final: 0.5837 (ptt)
REVERT: A  386 ARG cc_start: 0.8166 (mmt-90) cc_final: 0.5920 (mtt180)
REVERT: A  492 THR cc_start: 0.5628 (t) cc_final: 0.5405 (t)
REVERT: A  603 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7529 (tp30)
REVERT: A  621 MET cc_start: 0.6533 (mmm) cc_final: 0.5706 (mtt)
REVERT: A  644 GLU cc_start: 0.7750 (pp20) cc_final: 0.7266 (mp0)
REVERT: A  677 TRP cc_start: 0.4977 (m-10) cc_final: 0.4768 (m-10)
REVERT: A  692 ASN cc_start: 0.7028 (t0) cc_final: 0.6388 (t0)
REVERT: B  220 ASN cc_start: 0.8393 (m-40) cc_final: 0.8036 (m-40)
REVERT: B  336 ILE cc_start: 0.8166 (mm) cc_final: 0.7921 (mm)
REVERT: B  352 MET cc_start: 0.6679 (ptt) cc_final: 0.6288 (ptp)
REVERT: B  355 LYS cc_start: 0.7486 (mmpt) cc_final: 0.6912 (ptpt)
REVERT: B  472 MET cc_start: 0.8450 (tpp) cc_final: 0.7979 (mtt)
REVERT: B  492 THR cc_start: 0.5692 (t) cc_final: 0.5475 (t)
REVERT: B  501 MET cc_start: 0.7634 (mmp) cc_final: 0.7307 (mmp)
REVERT: B  570 CYS cc_start: 0.8847 (p) cc_final: 0.8576 (p)
REVERT: B  603 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7555 (tp30)
REVERT: B  621 MET cc_start: 0.6297 (mmm) cc_final: 0.5965 (mmm)
REVERT: B  692 ASN cc_start: 0.7191 (m-40) cc_final: 0.6880 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1069
  time to fit residues: 35.8172
Evaluate side-chains
  194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 89 optimal weight:    0.2980
   chunk 50 optimal weight:    0.0980
   chunk 52 optimal weight:    0.8980
   chunk 135 optimal weight:    0.8980
   chunk 117 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0010
   chunk 8 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   chunk 140 optimal weight:    0.7980
   chunk 66 optimal weight:    7.9990
   overall best weight:    0.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 GLN
B 193 GLN
** B 224 GLN ** 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 = 0.4419 r_free = 0.4419 target = 0.173201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.142778 restraints weight = 25081.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.146293 restraints weight = 16385.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.148660 restraints weight = 11966.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.150434 restraints weight = 9574.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.151649 restraints weight = 8139.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.8757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11116  Z= 0.126
  Angle     :  0.682   8.069  15082  Z= 0.357
  Chirality :  0.048   0.220   1768
  Planarity :  0.005   0.069   1964
  Dihedral  :  6.639  49.813   1620
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.58 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.22), residues: 1434
  helix:  0.29 (0.24), residues: 480
  sheet: -0.23 (0.40), residues: 154
  loop : -1.75 (0.22), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 159 
 TYR   0.012   0.001   TYR B 156 
 PHE   0.019   0.002   PHE B 153 
 TRP   0.005   0.001   TRP B 677 
 HIS   0.010   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (11116)
  covalent geometry    : angle       0.68193 (15082)
  hydrogen bonds       : bond        0.03555 (  424)
  hydrogen bonds       : angle       5.65437 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 TYR cc_start: 0.6289 (m-80) cc_final: 0.6064 (m-80)
REVERT: A   89 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8062 (mtm180)
REVERT: A  170 VAL cc_start: 0.8734 (t) cc_final: 0.8300 (p)
REVERT: A  336 ILE cc_start: 0.8206 (mm) cc_final: 0.7925 (mm)
REVERT: A  352 MET cc_start: 0.6221 (ptp) cc_final: 0.5827 (ptt)
REVERT: A  603 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7505 (tp30)
REVERT: A  621 MET cc_start: 0.6534 (mmm) cc_final: 0.6319 (mmm)
REVERT: A  644 GLU cc_start: 0.7654 (pp20) cc_final: 0.7163 (mp0)
REVERT: A  692 ASN cc_start: 0.7149 (t0) cc_final: 0.6460 (t0)
REVERT: B   89 ARG cc_start: 0.8905 (mtp180) cc_final: 0.7825 (mtm180)
REVERT: B  220 ASN cc_start: 0.8237 (m-40) cc_final: 0.8022 (m-40)
REVERT: B  336 ILE cc_start: 0.8264 (mm) cc_final: 0.8015 (mm)
REVERT: B  352 MET cc_start: 0.6781 (ptt) cc_final: 0.6315 (ptp)
REVERT: B  355 LYS cc_start: 0.7343 (mmpt) cc_final: 0.7047 (ptpt)
REVERT: B  472 MET cc_start: 0.8481 (tpp) cc_final: 0.7926 (mtt)
REVERT: B  501 MET cc_start: 0.7354 (mmp) cc_final: 0.7130 (mmp)
REVERT: B  603 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7637 (tp30)
REVERT: B  621 MET cc_start: 0.6209 (mmm) cc_final: 0.5964 (mmm)
REVERT: B  692 ASN cc_start: 0.7049 (m-40) cc_final: 0.6666 (t0)
REVERT: B  694 GLU cc_start: 0.8685 (pm20) cc_final: 0.8181 (pm20)
REVERT: B  695 ASN cc_start: 0.8878 (m110) cc_final: 0.8419 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.1081
  time to fit residues: 36.8170
Evaluate side-chains
  186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 10 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 132 optimal weight:    0.0000
   chunk 37 optimal weight:    0.2980
   chunk 76 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0670
   chunk 72 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.3322

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.173426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.143490 restraints weight = 24661.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.146728 restraints weight = 16348.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.149050 restraints weight = 12112.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.150737 restraints weight = 9750.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.151874 restraints weight = 8345.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6622
moved from start:          0.9046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11116  Z= 0.126
  Angle     :  0.693   9.597  15082  Z= 0.359
  Chirality :  0.047   0.240   1768
  Planarity :  0.005   0.071   1964
  Dihedral  :  6.517  49.553   1620
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.07 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.22), residues: 1434
  helix:  0.00 (0.23), residues: 490
  sheet: -0.61 (0.38), residues: 180
  loop : -1.71 (0.22), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 483 
 TYR   0.011   0.001   TYR B 156 
 PHE   0.019   0.002   PHE B 153 
 TRP   0.004   0.001   TRP A 180 
 HIS   0.008   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (11116)
  covalent geometry    : angle       0.69270 (15082)
  hydrogen bonds       : bond        0.03594 (  424)
  hydrogen bonds       : angle       5.66150 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ARG cc_start: 0.8846 (mtm180) cc_final: 0.8119 (mtm180)
REVERT: A  170 VAL cc_start: 0.8738 (t) cc_final: 0.8304 (p)
REVERT: A  336 ILE cc_start: 0.8146 (mm) cc_final: 0.7869 (mm)
REVERT: A  352 MET cc_start: 0.6247 (ptp) cc_final: 0.6018 (ptt)
REVERT: A  492 THR cc_start: 0.5682 (t) cc_final: 0.5470 (t)
REVERT: A  501 MET cc_start: 0.7204 (mmm) cc_final: 0.6897 (mmm)
REVERT: A  621 MET cc_start: 0.6402 (mmm) cc_final: 0.5696 (mtt)
REVERT: A  644 GLU cc_start: 0.7433 (pp20) cc_final: 0.7055 (mp0)
REVERT: A  692 ASN cc_start: 0.7115 (t0) cc_final: 0.6507 (t0)
REVERT: B   83 LEU cc_start: 0.7568 (mm) cc_final: 0.7283 (mm)
REVERT: B   89 ARG cc_start: 0.8857 (mtp180) cc_final: 0.8603 (mtt180)
REVERT: B  170 VAL cc_start: 0.8726 (t) cc_final: 0.8147 (p)
REVERT: B  336 ILE cc_start: 0.8231 (mm) cc_final: 0.7992 (mm)
REVERT: B  352 MET cc_start: 0.6858 (ptt) cc_final: 0.6297 (ptp)
REVERT: B  355 LYS cc_start: 0.7330 (mmpt) cc_final: 0.7080 (ptpt)
REVERT: B  472 MET cc_start: 0.8305 (tpp) cc_final: 0.8018 (mtt)
REVERT: B  603 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7569 (tp30)
REVERT: B  692 ASN cc_start: 0.7021 (m-40) cc_final: 0.6635 (t0)
REVERT: B  694 GLU cc_start: 0.8593 (pm20) cc_final: 0.8098 (pm20)
REVERT: B  695 ASN cc_start: 0.8854 (m110) cc_final: 0.8333 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1133
  time to fit residues: 37.6340
Evaluate side-chains
  185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 37 optimal weight:    0.3980
   chunk 59 optimal weight:    0.0870
   chunk 58 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.172250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.142066 restraints weight = 26490.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.145104 restraints weight = 18229.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.147276 restraints weight = 13818.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.148793 restraints weight = 11309.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.149630 restraints weight = 9815.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.9356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11116  Z= 0.135
  Angle     :  0.693   7.680  15082  Z= 0.362
  Chirality :  0.048   0.205   1768
  Planarity :  0.005   0.073   1964
  Dihedral  :  6.606  51.544   1620
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.14 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.22), residues: 1434
  helix: -0.05 (0.23), residues: 492
  sheet: -0.59 (0.38), residues: 180
  loop : -1.84 (0.22), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 483 
 TYR   0.010   0.001   TYR A 617 
 PHE   0.020   0.002   PHE B 153 
 TRP   0.007   0.001   TRP A 677 
 HIS   0.007   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (11116)
  covalent geometry    : angle       0.69289 (15082)
  hydrogen bonds       : bond        0.03593 (  424)
  hydrogen bonds       : angle       5.69236 ( 1128)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 LEU cc_start: 0.7531 (mm) cc_final: 0.7239 (mm)
REVERT: A   89 ARG cc_start: 0.8818 (mtm180) cc_final: 0.8324 (mtt180)
REVERT: A  170 VAL cc_start: 0.8778 (t) cc_final: 0.8350 (p)
REVERT: A  336 ILE cc_start: 0.8151 (mm) cc_final: 0.7839 (mm)
REVERT: A  352 MET cc_start: 0.6056 (ptp) cc_final: 0.5855 (ptt)
REVERT: A  474 MET cc_start: 0.9170 (ppp) cc_final: 0.8900 (ppp)
REVERT: A  492 THR cc_start: 0.5894 (t) cc_final: 0.5620 (t)
REVERT: A  541 MET cc_start: 0.7595 (mmp) cc_final: 0.6964 (mmm)
REVERT: A  621 MET cc_start: 0.6194 (mmm) cc_final: 0.5534 (mtt)
REVERT: A  644 GLU cc_start: 0.7563 (pp20) cc_final: 0.6761 (tp30)
REVERT: A  677 TRP cc_start: 0.4220 (m-10) cc_final: 0.4017 (m-10)
REVERT: A  692 ASN cc_start: 0.7142 (t0) cc_final: 0.6357 (t0)
REVERT: B   83 LEU cc_start: 0.7641 (mm) cc_final: 0.7375 (mm)
REVERT: B  336 ILE cc_start: 0.8277 (mm) cc_final: 0.8030 (mm)
REVERT: B  472 MET cc_start: 0.8497 (tpp) cc_final: 0.8231 (mtt)
REVERT: B  541 MET cc_start: 0.7627 (mmp) cc_final: 0.7395 (mmp)
REVERT: B  692 ASN cc_start: 0.7051 (m-40) cc_final: 0.6630 (t0)
REVERT: B  694 GLU cc_start: 0.8649 (pm20) cc_final: 0.8136 (pm20)
REVERT: B  695 ASN cc_start: 0.8849 (m110) cc_final: 0.8314 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1107
  time to fit residues: 34.6183
Evaluate side-chains
  185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 137 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 134 optimal weight:    3.9990
   chunk 122 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 ASN
A 624 HIS
B  34 GLN
B 143 GLN
** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 GLN
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 264 ASN
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.158547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.128581 restraints weight = 27073.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.131015 restraints weight = 19432.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.132698 restraints weight = 15236.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.133962 restraints weight = 12802.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.134696 restraints weight = 11306.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          1.0288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  11116  Z= 0.296
  Angle     :  0.938  10.081  15082  Z= 0.497
  Chirality :  0.053   0.247   1768
  Planarity :  0.007   0.080   1964
  Dihedral  :  8.344  59.029   1620
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 21.17
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.06 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.21), residues: 1434
  helix: -0.97 (0.22), residues: 488
  sheet: -0.38 (0.39), residues: 172
  loop : -2.29 (0.21), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 483 
 TYR   0.043   0.003   TYR B 617 
 PHE   0.039   0.004   PHE A 153 
 TRP   0.008   0.002   TRP B 677 
 HIS   0.015   0.002   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 (11116)
  covalent geometry    : angle       0.93793 (15082)
  hydrogen bonds       : bond        0.04983 (  424)
  hydrogen bonds       : angle       6.30023 ( 1128)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1958.22 seconds
wall clock time: 34 minutes 33.04 seconds (2073.04 seconds total)