Starting phenix.real_space_refine
on Tue Jul 29 07:12:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lgm_23327/07_2025/7lgm_23327.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lgm_23327/07_2025/7lgm_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_23327/07_2025/7lgm_23327.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lgm_23327/07_2025/7lgm_23327.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lgm_23327/07_2025/7lgm_23327.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lgm_23327/07_2025/7lgm_23327.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.053
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.98, per 1000 atoms: 1.00
  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: 2.54
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.45
  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: 3.32

  Time building geometry restraints manager: 3.03 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: 0.05
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:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     31.180
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.010
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (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
 TRP   0.017   0.006   TRP A 180 
 HIS   0.007   0.002   HIS B 679 
 PHE   0.015   0.006   PHE A 153 
 TYR   0.055   0.010   TYR A 196 
 ARG   0.011   0.001   ARG B 438 

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

*********************** 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  : 1.162 
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: 0.8048 (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: 0.4762 (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: 0.7096 (t70) cc_final: 0.6788 (t70)
REVERT: A  697 MET cc_start: 0.5428 (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: 0.8142 (m-40) cc_final: 0.7686 (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: 0.7501 (mmm-85)
REVERT: B  421 LEU cc_start: 0.8834 (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: 0.5261 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 417
  average time/residue: 0.2626
  time to fit residues: 147.0815
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  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 111 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 128 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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  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  63 HIS ** 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 = 0.4592 r_free = 0.4592 target = 0.185559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.158358 restraints weight = 27696.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.161652 restraints weight = 19120.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.164020 restraints weight = 14435.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6348
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11116  Z= 0.180
  Angle     :  0.790   9.261  15082  Z= 0.423
  Chirality :  0.048   0.246   1768
  Planarity :  0.005   0.072   1964
  Dihedral  :  7.208  58.499   1620
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.93 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.21), residues: 1434
  helix:  0.09 (0.23), residues: 472
  sheet: -0.33 (0.39), residues: 190
  loop : -1.33 (0.22), residues: 772

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04760 (  424)
  hydrogen bonds       : angle       6.29940 ( 1128)
  covalent geometry    : bond        0.00386 (11116)
  covalent geometry    : angle       0.78978 (15082)

*********************** 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
  314 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 312
  time to evaluate  : 1.254 
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: A   53 LEU cc_start: 0.8749 (mt) cc_final: 0.7857 (mt)
REVERT: A   89 ARG cc_start: 0.8267 (mtt180) cc_final: 0.8007 (mtt180)
REVERT: A  170 VAL cc_start: 0.8764 (t) cc_final: 0.8211 (p)
REVERT: A  336 ILE cc_start: 0.8145 (mm) cc_final: 0.7871 (mm)
REVERT: A  385 LEU cc_start: 0.7586 (mm) cc_final: 0.6957 (tp)
REVERT: A  404 ILE cc_start: 0.5037 (mm) cc_final: 0.4482 (tt)
REVERT: A  409 LYS cc_start: 0.7147 (mtmt) cc_final: 0.6611 (mtpt)
REVERT: A  508 MET cc_start: 0.6807 (mmp) cc_final: 0.6172 (mtt)
REVERT: A  555 THR cc_start: 0.8000 (t) cc_final: 0.7713 (t)
REVERT: A  577 ASN cc_start: 0.7753 (t0) cc_final: 0.7336 (p0)
REVERT: A  695 ASN cc_start: 0.8897 (m-40) cc_final: 0.8617 (m110)
REVERT: B   53 LEU cc_start: 0.8758 (mt) cc_final: 0.7814 (mt)
REVERT: B   89 ARG cc_start: 0.8193 (mtt180) cc_final: 0.7963 (mtt180)
REVERT: B  170 VAL cc_start: 0.8781 (t) cc_final: 0.8249 (p)
REVERT: B  336 ILE cc_start: 0.8032 (mm) cc_final: 0.7763 (mm)
REVERT: B  385 LEU cc_start: 0.7631 (mm) cc_final: 0.6943 (tp)
REVERT: B  386 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.6279 (mtt180)
REVERT: B  404 ILE cc_start: 0.5138 (mm) cc_final: 0.4584 (tt)
REVERT: B  409 LYS cc_start: 0.7204 (mtmt) cc_final: 0.6611 (mtpt)
REVERT: B  508 MET cc_start: 0.6873 (mmp) cc_final: 0.6344 (mtt)
REVERT: B  555 THR cc_start: 0.8249 (t) cc_final: 0.7944 (p)
REVERT: B  570 CYS cc_start: 0.8521 (p) cc_final: 0.8309 (p)
REVERT: B  577 ASN cc_start: 0.7835 (t0) cc_final: 0.7276 (p0)
REVERT: B  645 HIS cc_start: 0.7054 (t70) cc_final: 0.6398 (t70)
REVERT: B  692 ASN cc_start: 0.6639 (m-40) cc_final: 0.6263 (t0)
REVERT: B  695 ASN cc_start: 0.8938 (m-40) cc_final: 0.8680 (m110)
  outliers start: 2
  outliers final: 2
  residues processed: 314
  average time/residue: 0.2399
  time to fit residues: 104.4589
Evaluate side-chains
  209 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 207
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 110 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 135 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.7762

-------------------------------------------------------------------------------
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 143 GLN
A 193 GLN
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 143 GLN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.176559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.147082 restraints weight = 25163.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.150709 restraints weight = 16646.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.153308 restraints weight = 12134.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6511
moved from start:          0.5801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11116  Z= 0.173
  Angle     :  0.749   8.016  15082  Z= 0.399
  Chirality :  0.049   0.369   1768
  Planarity :  0.005   0.081   1964
  Dihedral  :  7.103  50.396   1620
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.02 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.21), residues: 1434
  helix:  0.14 (0.23), residues: 480
  sheet: -0.62 (0.40), residues: 170
  loop : -1.60 (0.21), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 677 
 HIS   0.006   0.001   HIS B 645 
 PHE   0.024   0.003   PHE B 698 
 TYR   0.022   0.002   TYR B 156 
 ARG   0.009   0.001   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04284 (  424)
  hydrogen bonds       : angle       6.03969 ( 1128)
  covalent geometry    : bond        0.00359 (11116)
  covalent geometry    : angle       0.74891 (15082)

*********************** 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
  271 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 270
  time to evaluate  : 1.150 
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  170 VAL cc_start: 0.8765 (t) cc_final: 0.8376 (p)
REVERT: A  220 ASN cc_start: 0.8251 (m-40) cc_final: 0.7523 (m-40)
REVERT: A  336 ILE cc_start: 0.8076 (mm) cc_final: 0.7793 (mm)
REVERT: A  352 MET cc_start: 0.5871 (ptp) cc_final: 0.5543 (ptt)
REVERT: A  355 LYS cc_start: 0.7508 (tppt) cc_final: 0.6802 (ptmt)
REVERT: A  385 LEU cc_start: 0.7514 (mm) cc_final: 0.6949 (tt)
REVERT: A  386 ARG cc_start: 0.7962 (mmt-90) cc_final: 0.6955 (mtt180)
REVERT: A  492 THR cc_start: 0.6512 (p) cc_final: 0.6240 (p)
REVERT: A  501 MET cc_start: 0.8161 (mmt) cc_final: 0.7955 (mmm)
REVERT: A  508 MET cc_start: 0.7092 (mmp) cc_final: 0.6425 (mtp)
REVERT: A  570 CYS cc_start: 0.8602 (p) cc_final: 0.8337 (p)
REVERT: A  692 ASN cc_start: 0.6588 (t0) cc_final: 0.6049 (t0)
REVERT: B  119 ILE cc_start: 0.6697 (pt) cc_final: 0.6151 (pt)
REVERT: B  170 VAL cc_start: 0.8804 (t) cc_final: 0.8437 (p)
REVERT: B  220 ASN cc_start: 0.8337 (m-40) cc_final: 0.7654 (m-40)
REVERT: B  336 ILE cc_start: 0.8126 (mm) cc_final: 0.7881 (mm)
REVERT: B  352 MET cc_start: 0.6144 (ptp) cc_final: 0.5781 (ptt)
REVERT: B  355 LYS cc_start: 0.7598 (mmmt) cc_final: 0.6751 (ptpt)
REVERT: B  385 LEU cc_start: 0.7720 (mm) cc_final: 0.7186 (tt)
REVERT: B  386 ARG cc_start: 0.7772 (mmt-90) cc_final: 0.5651 (mtt180)
REVERT: B  409 LYS cc_start: 0.7223 (mtmt) cc_final: 0.6713 (mtpt)
REVERT: B  448 ASN cc_start: 0.7606 (t0) cc_final: 0.6815 (m-40)
REVERT: B  508 MET cc_start: 0.7263 (mmp) cc_final: 0.6529 (mtp)
REVERT: B  692 ASN cc_start: 0.6996 (m-40) cc_final: 0.6503 (t0)
REVERT: B  695 ASN cc_start: 0.9029 (m-40) cc_final: 0.8782 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 270
  average time/residue: 0.2591
  time to fit residues: 95.8484
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  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 80 optimal weight:    8.9990
   chunk 27 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 24 optimal weight:    0.4980
   chunk 127 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
A 645 HIS
** A 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 GLN
B 405 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.171724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.141845 restraints weight = 25016.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.144999 restraints weight = 16887.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.147229 restraints weight = 12616.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.6936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11116  Z= 0.157
  Angle     :  0.707   7.217  15082  Z= 0.377
  Chirality :  0.048   0.282   1768
  Planarity :  0.005   0.076   1964
  Dihedral  :  7.146  51.127   1620
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.79 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.21), residues: 1434
  helix:  0.18 (0.23), residues: 482
  sheet: -0.69 (0.42), residues: 152
  loop : -1.75 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 180 
 HIS   0.009   0.001   HIS B 645 
 PHE   0.020   0.002   PHE B 153 
 TYR   0.018   0.002   TYR B 156 
 ARG   0.007   0.001   ARG B 562 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03856 (  424)
  hydrogen bonds       : angle       5.85409 ( 1128)
  covalent geometry    : bond        0.00340 (11116)
  covalent geometry    : angle       0.70738 (15082)

*********************** 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
  239 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.188 
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: A  170 VAL cc_start: 0.8764 (t) cc_final: 0.8240 (p)
REVERT: A  220 ASN cc_start: 0.8620 (m-40) cc_final: 0.7795 (m-40)
REVERT: A  336 ILE cc_start: 0.8204 (mm) cc_final: 0.7930 (mm)
REVERT: A  352 MET cc_start: 0.5822 (ptp) cc_final: 0.5495 (ptt)
REVERT: A  355 LYS cc_start: 0.7666 (tppt) cc_final: 0.7000 (ptmt)
REVERT: A  386 ARG cc_start: 0.8279 (mmt-90) cc_final: 0.6368 (mtm-85)
REVERT: A  430 THR cc_start: 0.8911 (t) cc_final: 0.8701 (m)
REVERT: A  492 THR cc_start: 0.6621 (p) cc_final: 0.6387 (p)
REVERT: A  644 GLU cc_start: 0.7704 (pp20) cc_final: 0.7434 (mp0)
REVERT: A  692 ASN cc_start: 0.6963 (t0) cc_final: 0.6239 (t0)
REVERT: A  702 MET cc_start: 0.8495 (mmm) cc_final: 0.8142 (mmm)
REVERT: B  170 VAL cc_start: 0.8781 (t) cc_final: 0.8408 (p)
REVERT: B  220 ASN cc_start: 0.8521 (m-40) cc_final: 0.7789 (m-40)
REVERT: B  336 ILE cc_start: 0.8019 (mm) cc_final: 0.7756 (mm)
REVERT: B  352 MET cc_start: 0.5947 (ptp) cc_final: 0.5640 (ptt)
REVERT: B  492 THR cc_start: 0.6645 (p) cc_final: 0.6430 (p)
REVERT: B  508 MET cc_start: 0.7610 (mmp) cc_final: 0.6991 (mtp)
REVERT: B  541 MET cc_start: 0.7969 (mmp) cc_final: 0.7757 (mmp)
REVERT: B  621 MET cc_start: 0.6618 (mmm) cc_final: 0.6414 (mmm)
REVERT: B  692 ASN cc_start: 0.6930 (m-40) cc_final: 0.6545 (t0)
REVERT: B  695 ASN cc_start: 0.8952 (m-40) cc_final: 0.8603 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2450
  time to fit residues: 82.4904
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  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 116 optimal weight:    0.4980
   chunk 51 optimal weight:    0.0670
   chunk 28 optimal weight:    0.5980
   chunk 102 optimal weight:    2.9990
   chunk 127 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 112 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 137 optimal weight:    5.9990
   overall best weight:    0.5720

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
A 193 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN
B 190 GLN
B 193 GLN
** B 405 HIS ** 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 = 0.4403 r_free = 0.4403 target = 0.172279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.141609 restraints weight = 25181.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.144852 restraints weight = 16879.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.147201 restraints weight = 12551.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.7520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11116  Z= 0.138
  Angle     :  0.682   8.016  15082  Z= 0.361
  Chirality :  0.047   0.202   1768
  Planarity :  0.005   0.072   1964
  Dihedral  :  6.978  51.011   1620
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.51 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.22), residues: 1434
  helix:  0.25 (0.23), residues: 480
  sheet: -0.77 (0.39), residues: 174
  loop : -1.70 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 180 
 HIS   0.007   0.001   HIS A  86 
 PHE   0.021   0.003   PHE B 153 
 TYR   0.025   0.001   TYR B 156 
 ARG   0.010   0.000   ARG A 483 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  424)
  hydrogen bonds       : angle       5.86627 ( 1128)
  covalent geometry    : bond        0.00295 (11116)
  covalent geometry    : angle       0.68207 (15082)

*********************** 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
  234 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.226 
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: 0.8805 (t) cc_final: 0.8281 (p)
REVERT: A  220 ASN cc_start: 0.8352 (m-40) cc_final: 0.8081 (m-40)
REVERT: A  336 ILE cc_start: 0.8206 (mm) cc_final: 0.7902 (mm)
REVERT: A  352 MET cc_start: 0.5800 (ptp) cc_final: 0.5528 (ptt)
REVERT: A  355 LYS cc_start: 0.7727 (tppt) cc_final: 0.6938 (ptmt)
REVERT: A  409 LYS cc_start: 0.7498 (mtmt) cc_final: 0.6989 (ptmt)
REVERT: A  430 THR cc_start: 0.8961 (t) cc_final: 0.8605 (m)
REVERT: A  472 MET cc_start: 0.8393 (tpp) cc_final: 0.7939 (mtt)
REVERT: A  603 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7515 (mm-30)
REVERT: A  611 LEU cc_start: 0.9354 (mm) cc_final: 0.8992 (mm)
REVERT: A  692 ASN cc_start: 0.7024 (t0) cc_final: 0.6326 (t0)
REVERT: A  697 MET cc_start: 0.8034 (mtm) cc_final: 0.7773 (mtp)
REVERT: B  220 ASN cc_start: 0.8246 (m-40) cc_final: 0.7696 (m-40)
REVERT: B  336 ILE cc_start: 0.8068 (mm) cc_final: 0.7831 (mm)
REVERT: B  352 MET cc_start: 0.5967 (ptp) cc_final: 0.5702 (ptt)
REVERT: B  692 ASN cc_start: 0.7227 (m-40) cc_final: 0.6988 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.2358
  time to fit residues: 77.4234
Evaluate side-chains
  183 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 140 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 133 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 127 optimal weight:    0.0270
   overall best weight:    0.7638

-------------------------------------------------------------------------------
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 193 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 695 ASN
** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.170153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.139205 restraints weight = 25480.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.142387 restraints weight = 17059.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.144683 restraints weight = 12724.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.8142

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= 0.147
  Angle     :  0.684   8.074  15082  Z= 0.361
  Chirality :  0.048   0.249   1768
  Planarity :  0.005   0.072   1964
  Dihedral  :  7.008  52.446   1620
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.07 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.22), residues: 1434
  helix:  0.25 (0.24), residues: 476
  sheet: -0.63 (0.40), residues: 164
  loop : -1.86 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 180 
 HIS   0.017   0.001   HIS A  30 
 PHE   0.022   0.003   PHE B 153 
 TYR   0.026   0.001   TYR B 156 
 ARG   0.008   0.000   ARG A 483 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (  424)
  hydrogen bonds       : angle       5.90780 ( 1128)
  covalent geometry    : bond        0.00313 (11116)
  covalent geometry    : angle       0.68417 (15082)

*********************** 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
  231 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.6310 (mmt) cc_final: 0.5968 (mmt)
REVERT: A  156 TYR cc_start: 0.7517 (m-10) cc_final: 0.7216 (m-80)
REVERT: A  170 VAL cc_start: 0.8875 (t) cc_final: 0.8452 (p)
REVERT: A  336 ILE cc_start: 0.8317 (mm) cc_final: 0.8077 (mm)
REVERT: A  352 MET cc_start: 0.5829 (ptp) cc_final: 0.5471 (ptt)
REVERT: A  402 ASP cc_start: 0.7961 (p0) cc_final: 0.7737 (p0)
REVERT: A  409 LYS cc_start: 0.7482 (mtmt) cc_final: 0.7106 (ptmt)
REVERT: A  508 MET cc_start: 0.8094 (mtm) cc_final: 0.7856 (mtm)
REVERT: A  692 ASN cc_start: 0.7256 (t0) cc_final: 0.6541 (t0)
REVERT: A  702 MET cc_start: 0.8577 (mmm) cc_final: 0.8291 (mmm)
REVERT: B   53 LEU cc_start: 0.8690 (mt) cc_final: 0.7962 (mt)
REVERT: B  130 MET cc_start: 0.6409 (mmt) cc_final: 0.6090 (mmt)
REVERT: B  170 VAL cc_start: 0.8787 (t) cc_final: 0.8335 (p)
REVERT: B  220 ASN cc_start: 0.8277 (m-40) cc_final: 0.7871 (m-40)
REVERT: B  336 ILE cc_start: 0.8141 (mm) cc_final: 0.7905 (mm)
REVERT: B  355 LYS cc_start: 0.7583 (mmpt) cc_final: 0.7088 (ptpt)
REVERT: B  611 LEU cc_start: 0.9316 (mm) cc_final: 0.8918 (mm)
REVERT: B  692 ASN cc_start: 0.7560 (m-40) cc_final: 0.7280 (t0)
REVERT: B  695 ASN cc_start: 0.8762 (m110) cc_final: 0.8512 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.2359
  time to fit residues: 76.7476
Evaluate side-chains
  182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 22 optimal weight:    0.1980
   chunk 92 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0060
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 80 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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**
A 504 HIS
B 143 GLN
B 193 GLN
B 405 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.171882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.141017 restraints weight = 25525.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.144229 restraints weight = 17105.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.146575 restraints weight = 12780.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.8548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11116  Z= 0.133
  Angle     :  0.689  10.558  15082  Z= 0.359
  Chirality :  0.047   0.186   1768
  Planarity :  0.005   0.073   1964
  Dihedral  :  6.926  50.498   1620
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.00 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.22), residues: 1434
  helix:  0.11 (0.23), residues: 494
  sheet: -0.45 (0.40), residues: 160
  loop : -1.94 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 180 
 HIS   0.007   0.001   HIS A 504 
 PHE   0.029   0.003   PHE B 698 
 TYR   0.028   0.001   TYR B 156 
 ARG   0.010   0.001   ARG A 483 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03653 (  424)
  hydrogen bonds       : angle       5.91479 ( 1128)
  covalent geometry    : bond        0.00286 (11116)
  covalent geometry    : angle       0.68911 (15082)

*********************** 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
  245 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.148 
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  170 VAL cc_start: 0.8805 (t) cc_final: 0.8357 (p)
REVERT: A  336 ILE cc_start: 0.8227 (mm) cc_final: 0.8000 (mm)
REVERT: A  692 ASN cc_start: 0.7211 (t0) cc_final: 0.6597 (t0)
REVERT: B  170 VAL cc_start: 0.8750 (t) cc_final: 0.8236 (p)
REVERT: B  220 ASN cc_start: 0.8270 (m-40) cc_final: 0.7882 (m-40)
REVERT: B  336 ILE cc_start: 0.8078 (mm) cc_final: 0.7850 (mm)
REVERT: B  352 MET cc_start: 0.6567 (ptt) cc_final: 0.6132 (ptp)
REVERT: B  355 LYS cc_start: 0.7614 (mmpt) cc_final: 0.7101 (ptpt)
REVERT: B  430 THR cc_start: 0.9033 (t) cc_final: 0.8733 (m)
REVERT: B  472 MET cc_start: 0.8356 (tpp) cc_final: 0.7945 (mtt)
REVERT: B  603 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7347 (tp30)
REVERT: B  694 GLU cc_start: 0.8523 (pm20) cc_final: 0.8092 (pm20)
REVERT: B  702 MET cc_start: 0.8671 (mmm) cc_final: 0.8375 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2159
  time to fit residues: 75.6590
Evaluate side-chains
  195 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 13 optimal weight:    9.9990
   chunk 65 optimal weight:    9.9990
   chunk 98 optimal weight:    1.9990
   chunk 121 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0970
   chunk 26 optimal weight:    5.9990
   chunk 4 optimal weight:    0.5980
   chunk 125 optimal weight:    2.9990
   chunk 128 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 143 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.170739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.139953 restraints weight = 26433.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.142992 restraints weight = 17967.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.145224 restraints weight = 13560.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6803
moved from start:          0.9032

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= 0.140
  Angle     :  0.690  12.313  15082  Z= 0.363
  Chirality :  0.048   0.239   1768
  Planarity :  0.005   0.075   1964
  Dihedral  :  6.919  53.116   1620
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.27 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.21), residues: 1434
  helix: -0.15 (0.23), residues: 510
  sheet: -0.35 (0.41), residues: 160
  loop : -2.10 (0.21), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 180 
 HIS   0.006   0.001   HIS B  86 
 PHE   0.021   0.002   PHE B 698 
 TYR   0.028   0.001   TYR B 156 
 ARG   0.009   0.001   ARG A 483 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03683 (  424)
  hydrogen bonds       : angle       5.89225 ( 1128)
  covalent geometry    : bond        0.00299 (11116)
  covalent geometry    : angle       0.69017 (15082)

*********************** 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
  247 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 VAL cc_start: 0.8755 (t) cc_final: 0.8238 (p)
REVERT: A  336 ILE cc_start: 0.8362 (mm) cc_final: 0.8107 (mm)
REVERT: A  352 MET cc_start: 0.6910 (ptt) cc_final: 0.6387 (ptp)
REVERT: A  355 LYS cc_start: 0.7111 (tptm) cc_final: 0.6694 (ptmt)
REVERT: A  386 ARG cc_start: 0.8074 (mmt-90) cc_final: 0.6093 (mtm-85)
REVERT: A  472 MET cc_start: 0.8491 (tpp) cc_final: 0.7974 (mtt)
REVERT: A  692 ASN cc_start: 0.7501 (t0) cc_final: 0.7014 (t0)
REVERT: A  695 ASN cc_start: 0.8595 (m110) cc_final: 0.8302 (m-40)
REVERT: B   53 LEU cc_start: 0.8475 (mt) cc_final: 0.8251 (mt)
REVERT: B   88 GLN cc_start: 0.8087 (mt0) cc_final: 0.7815 (mt0)
REVERT: B  170 VAL cc_start: 0.8744 (t) cc_final: 0.8300 (p)
REVERT: B  220 ASN cc_start: 0.7975 (m-40) cc_final: 0.7731 (m-40)
REVERT: B  336 ILE cc_start: 0.8235 (mm) cc_final: 0.8028 (mm)
REVERT: B  355 LYS cc_start: 0.7690 (mmpt) cc_final: 0.7238 (ptpt)
REVERT: B  386 ARG cc_start: 0.8057 (mmt-90) cc_final: 0.6484 (mtt90)
REVERT: B  430 THR cc_start: 0.9071 (t) cc_final: 0.8713 (m)
REVERT: B  501 MET cc_start: 0.7323 (mmp) cc_final: 0.7063 (mmp)
REVERT: B  541 MET cc_start: 0.7718 (mmp) cc_final: 0.7491 (mmp)
REVERT: B  692 ASN cc_start: 0.6825 (t0) cc_final: 0.6308 (t0)
REVERT: B  694 GLU cc_start: 0.8565 (pm20) cc_final: 0.8033 (pm20)
REVERT: B  695 ASN cc_start: 0.8862 (m110) cc_final: 0.8472 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2288
  time to fit residues: 80.5925
Evaluate side-chains
  196 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 106 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0980
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 ASN
** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 GLN
B 264 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.169936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.139070 restraints weight = 26467.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.142139 restraints weight = 18091.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.144351 restraints weight = 13655.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
moved from start:          0.9430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11116  Z= 0.138
  Angle     :  0.701  11.156  15082  Z= 0.365
  Chirality :  0.047   0.192   1768
  Planarity :  0.005   0.074   1964
  Dihedral  :  6.980  53.941   1620
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.48 %
    Favored  : 90.38 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.21), residues: 1434
  helix: -0.24 (0.23), residues: 512
  sheet: -0.45 (0.40), residues: 170
  loop : -2.15 (0.21), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 677 
 HIS   0.005   0.001   HIS A  86 
 PHE   0.033   0.002   PHE B 698 
 TYR   0.037   0.001   TYR B 156 
 ARG   0.008   0.001   ARG A  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  424)
  hydrogen bonds       : angle       5.82827 ( 1128)
  covalent geometry    : bond        0.00294 (11116)
  covalent geometry    : angle       0.70068 (15082)

*********************** 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  : 1.326 
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: A  170 VAL cc_start: 0.8732 (t) cc_final: 0.8195 (p)
REVERT: A  336 ILE cc_start: 0.8298 (mm) cc_final: 0.8017 (mm)
REVERT: A  355 LYS cc_start: 0.7213 (tppp) cc_final: 0.6802 (ptmt)
REVERT: A  472 MET cc_start: 0.8630 (tpp) cc_final: 0.8137 (mtt)
REVERT: A  473 ASP cc_start: 0.8516 (m-30) cc_final: 0.8281 (m-30)
REVERT: A  692 ASN cc_start: 0.7472 (t0) cc_final: 0.7069 (t0)
REVERT: B  170 VAL cc_start: 0.8770 (t) cc_final: 0.8243 (p)
REVERT: B  220 ASN cc_start: 0.7982 (m-40) cc_final: 0.7603 (m-40)
REVERT: B  336 ILE cc_start: 0.8233 (mm) cc_final: 0.8011 (mm)
REVERT: B  355 LYS cc_start: 0.7651 (mmpt) cc_final: 0.7188 (ptpt)
REVERT: B  472 MET cc_start: 0.8675 (tpp) cc_final: 0.8248 (mtt)
REVERT: B  501 MET cc_start: 0.7211 (mmp) cc_final: 0.6935 (mmp)
REVERT: B  541 MET cc_start: 0.7833 (mmp) cc_final: 0.7610 (mmp)
REVERT: B  603 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7349 (tp30)
REVERT: B  692 ASN cc_start: 0.6713 (t0) cc_final: 0.6050 (t0)
REVERT: B  694 GLU cc_start: 0.8658 (pm20) cc_final: 0.8226 (pm20)
REVERT: B  695 ASN cc_start: 0.8870 (m110) cc_final: 0.8603 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2404
  time to fit residues: 79.7075
Evaluate side-chains
  193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 117 optimal weight:    0.0070
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 131 optimal weight:    0.0000
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.3602

-------------------------------------------------------------------------------
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 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 ASN
** A 695 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 = 0.4419 r_free = 0.4419 target = 0.172087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.141105 restraints weight = 26245.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.144249 restraints weight = 17872.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.146403 restraints weight = 13422.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6803
moved from start:          0.9716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  11116  Z= 0.127
  Angle     :  0.702  15.887  15082  Z= 0.363
  Chirality :  0.047   0.188   1768
  Planarity :  0.005   0.073   1964
  Dihedral  :  6.651  50.281   1620
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.55 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.21), residues: 1434
  helix: -0.18 (0.23), residues: 512
  sheet: -0.37 (0.42), residues: 170
  loop : -2.15 (0.21), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 180 
 HIS   0.004   0.001   HIS A  86 
 PHE   0.022   0.002   PHE B 698 
 TYR   0.036   0.001   TYR B 156 
 ARG   0.015   0.001   ARG A 483 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03547 (  424)
  hydrogen bonds       : angle       5.82581 ( 1128)
  covalent geometry    : bond        0.00267 (11116)
  covalent geometry    : angle       0.70174 (15082)

********************** 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
  238 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 1.201 
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: A  156 TYR cc_start: 0.7736 (m-80) cc_final: 0.7481 (m-80)
REVERT: A  170 VAL cc_start: 0.8685 (t) cc_final: 0.8191 (p)
REVERT: A  336 ILE cc_start: 0.8328 (mm) cc_final: 0.8055 (mm)
REVERT: A  386 ARG cc_start: 0.8004 (mmt-90) cc_final: 0.5783 (mtt180)
REVERT: A  430 THR cc_start: 0.8929 (t) cc_final: 0.8582 (m)
REVERT: A  472 MET cc_start: 0.8461 (tpp) cc_final: 0.7962 (mtt)
REVERT: A  541 MET cc_start: 0.7478 (mmp) cc_final: 0.7114 (mmm)
REVERT: A  603 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7018 (tp30)
REVERT: A  630 ILE cc_start: 0.8580 (mm) cc_final: 0.8321 (mm)
REVERT: A  692 ASN cc_start: 0.7121 (t0) cc_final: 0.6576 (t0)
REVERT: B   88 GLN cc_start: 0.8191 (mt0) cc_final: 0.7859 (tm-30)
REVERT: B  170 VAL cc_start: 0.8744 (t) cc_final: 0.8208 (p)
REVERT: B  220 ASN cc_start: 0.8018 (m-40) cc_final: 0.7609 (m-40)
REVERT: B  336 ILE cc_start: 0.8407 (mm) cc_final: 0.8157 (mm)
REVERT: B  355 LYS cc_start: 0.7524 (mmpt) cc_final: 0.7203 (ptpt)
REVERT: B  430 THR cc_start: 0.9021 (t) cc_final: 0.8648 (m)
REVERT: B  472 MET cc_start: 0.8429 (tpp) cc_final: 0.8205 (mtt)
REVERT: B  476 PHE cc_start: 0.8684 (m-80) cc_final: 0.8431 (m-10)
REVERT: B  501 MET cc_start: 0.7064 (mmp) cc_final: 0.6813 (mmp)
REVERT: B  603 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7268 (tp30)
REVERT: B  692 ASN cc_start: 0.6705 (t0) cc_final: 0.5938 (t0)
REVERT: B  694 GLU cc_start: 0.8679 (pm20) cc_final: 0.8198 (pm20)
REVERT: B  695 ASN cc_start: 0.8938 (m110) cc_final: 0.8591 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.2444
  time to fit residues: 83.8625
Evaluate side-chains
  193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 109 optimal weight:    0.0970
   chunk 42 optimal weight:    2.9990
   chunk 136 optimal weight:    0.3980
   chunk 140 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 112 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0470
   overall best weight:    0.4276

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  86 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.171711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.140661 restraints weight = 26361.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.143832 restraints weight = 17832.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.146047 restraints weight = 13361.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6824
moved from start:          1.0001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11116  Z= 0.130
  Angle     :  0.686  10.732  15082  Z= 0.357
  Chirality :  0.047   0.191   1768
  Planarity :  0.005   0.073   1964
  Dihedral  :  6.560  51.621   1620
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.18 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.22), residues: 1434
  helix: -0.16 (0.23), residues: 512
  sheet: -0.61 (0.40), residues: 188
  loop : -2.11 (0.22), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 180 
 HIS   0.009   0.001   HIS A 629 
 PHE   0.023   0.002   PHE A 476 
 TYR   0.036   0.001   TYR B 156 
 ARG   0.012   0.001   ARG A 483 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03483 (  424)
  hydrogen bonds       : angle       5.79876 ( 1128)
  covalent geometry    : bond        0.00274 (11116)
  covalent geometry    : angle       0.68565 (15082)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4580.34 seconds
wall clock time: 82 minutes 10.00 seconds (4930.00 seconds total)