Starting phenix.real_space_refine
on Thu Feb 13 15:58:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tve_41639/02_2025/8tve_41639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tve_41639/02_2025/8tve_41639.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tve_41639/02_2025/8tve_41639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tve_41639/02_2025/8tve_41639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tve_41639/02_2025/8tve_41639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tve_41639/02_2025/8tve_41639.cif"
  }
  resolution = 3.9
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5799      2.51       5
     N    1536      2.21       5
     O    1707      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9090
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3002
          Classifications: {'peptide': 409}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 15, 'TRANS': 393}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 116
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 73
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 2.83, per 1000 atoms: 0.31
  Number of scatterers: 9090
  At special positions: 0
  Unit cell: (84.96, 85.845, 171.69, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1707      8.00
     N    1536      7.00
     C    5799      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 187 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 412 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A  65 "
      " NAG A 602 " - " ASN A 459 "
      " NAG B 601 " - " ASN B  65 "
      " NAG B 602 " - " ASN B 459 "
      " NAG C 601 " - " ASN C  65 "
      " NAG C 602 " - " ASN C 459 "
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2310

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 18 sheets defined
      42.8% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 32
      removed outlier: 4.997A  pdb=" N   LYS A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 92
      Proline residue:  A  84  - end of helix
    Processing helix  chain 'A' and resid 141 through 178
    Processing helix  chain 'A' and resid 178 through 207
    Processing helix  chain 'A' and resid 209 through 215
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 233 through 242
    Processing helix  chain 'A' and resid 244 through 254
    Processing helix  chain 'A' and resid 344 through 353
      removed outlier: 4.237A  pdb=" N   CYS A 350 " --> pdb=" O   GLU A 346 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 476
    Processing helix  chain 'B' and resid 24 through 32
      removed outlier: 4.997A  pdb=" N   LYS B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 92
      Proline residue:  B  84  - end of helix
    Processing helix  chain 'B' and resid 141 through 178
    Processing helix  chain 'B' and resid 178 through 207
    Processing helix  chain 'B' and resid 209 through 215
    Processing helix  chain 'B' and resid 222 through 230
    Processing helix  chain 'B' and resid 233 through 242
    Processing helix  chain 'B' and resid 244 through 254
    Processing helix  chain 'B' and resid 344 through 353
      removed outlier: 4.237A  pdb=" N   CYS B 350 " --> pdb=" O   GLU B 346 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU B 351 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 476
    Processing helix  chain 'C' and resid 24 through 32
      removed outlier: 4.997A  pdb=" N   LYS C  30 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 92
      Proline residue:  C  84  - end of helix
    Processing helix  chain 'C' and resid 141 through 178
    Processing helix  chain 'C' and resid 178 through 207
    Processing helix  chain 'C' and resid 209 through 215
    Processing helix  chain 'C' and resid 222 through 230
    Processing helix  chain 'C' and resid 233 through 242
    Processing helix  chain 'C' and resid 244 through 254
    Processing helix  chain 'C' and resid 344 through 353
      removed outlier: 4.237A  pdb=" N   CYS C 350 " --> pdb=" O   GLU C 346 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU C 351 " --> pdb=" O   LEU C 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 476
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38
      removed outlier: 5.344A  pdb=" N   GLU A 290 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   THR A  38 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL A 288 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   PHE A 310 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE A 321 " --> pdb=" O   PHE A 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 281 through 282
    Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220
      removed outlier: 7.012A  pdb=" N   ALA A 272 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   VAL A 264 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   TYR A 270 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 8.957A  pdb=" N   GLY B 431 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU A  51 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   TYR B 433 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL A  53 " --> pdb=" O   TYR B 433 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298
    Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 374
      removed outlier: 4.031A  pdb=" N   VAL A 378 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 394 through 395
      removed outlier: 3.526A  pdb=" N   THR A 394 " --> pdb=" O   CYS A 389 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433
      removed outlier: 6.900A  pdb=" N   TYR C 270 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   VAL C 264 " --> pdb=" O   TYR C 270 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ALA C 272 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 38
      removed outlier: 5.345A  pdb=" N   GLU B 290 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   THR B  38 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL B 288 " --> pdb=" O   THR B  38 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   PHE B 310 " --> pdb=" O   ILE B 321 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B 321 " --> pdb=" O   PHE B 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 281 through 282
    Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220
      removed outlier: 7.012A  pdb=" N   ALA B 272 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   VAL B 264 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   TYR B 270 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 8.957A  pdb=" N   GLY C 431 " --> pdb=" O   THR B  49 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU B  51 " --> pdb=" O   GLY C 431 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   TYR C 433 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL B  53 " --> pdb=" O   TYR C 433 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 296 through 298
    Processing sheet with id=AB3, first strand: chain 'B' and resid 371 through 374
      removed outlier: 4.032A  pdb=" N   VAL B 378 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 394 through 395
      removed outlier: 3.525A  pdb=" N   THR B 394 " --> pdb=" O   CYS B 389 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 38
      removed outlier: 5.344A  pdb=" N   GLU C 290 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   THR C  38 " --> pdb=" O   VAL C 288 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL C 288 " --> pdb=" O   THR C  38 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   PHE C 310 " --> pdb=" O   ILE C 321 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE C 321 " --> pdb=" O   PHE C 310 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 281 through 282
    Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 298
    Processing sheet with id=AB8, first strand: chain 'C' and resid 371 through 374
      removed outlier: 4.031A  pdb=" N   VAL C 378 " --> pdb=" O   LEU C 407 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 394 through 395
      removed outlier: 3.525A  pdb=" N   THR C 394 " --> pdb=" O   CYS C 389 " (cutoff:3.500A)

    547 hydrogen bonds defined for protein.
    1530 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.93

  Time building geometry restraints manager: 2.58 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2310
        1.33 -     1.46: 2146
        1.46 -     1.59: 4691
        1.59 -     1.71: 3
        1.71 -     1.84: 66
  Bond restraints: 9216
  Sorted by residual:
  bond pdb=" CB  LEU A  23 "
       pdb=" CG  LEU A  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.602 -0.072 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" CB  LEU B  23 "
       pdb=" CG  LEU B  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.601 -0.071 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" CB  LEU C  23 "
       pdb=" CG  LEU C  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.601 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" NE  ARG C 171 "
       pdb=" CZ  ARG C 171 "
    ideal  model  delta    sigma   weight residual
    1.326  1.362 -0.036 1.10e-02 8.26e+03 1.07e+01
  bond pdb=" NE  ARG A 171 "
       pdb=" CZ  ARG A 171 "
    ideal  model  delta    sigma   weight residual
    1.326  1.362 -0.036 1.10e-02 8.26e+03 1.05e+01
  ... (remaining 9211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 11244
        2.28 -     4.56: 1059
        4.56 -     6.85: 225
        6.85 -     9.13: 33
        9.13 -    11.41: 12
  Bond angle restraints: 12573
  Sorted by residual:
  angle pdb=" N   ASN C 464 "
        pdb=" CA  ASN C 464 "
        pdb=" C   ASN C 464 "
      ideal   model   delta    sigma   weight residual
     111.36  101.68    9.68 1.09e+00 8.42e-01 7.89e+01
  angle pdb=" N   ASN B 464 "
        pdb=" CA  ASN B 464 "
        pdb=" C   ASN B 464 "
      ideal   model   delta    sigma   weight residual
     111.36  101.68    9.68 1.09e+00 8.42e-01 7.88e+01
  angle pdb=" N   ASN A 464 "
        pdb=" CA  ASN A 464 "
        pdb=" C   ASN A 464 "
      ideal   model   delta    sigma   weight residual
     111.36  101.69    9.67 1.09e+00 8.42e-01 7.88e+01
  angle pdb=" N   MET C 142 "
        pdb=" CA  MET C 142 "
        pdb=" C   MET C 142 "
      ideal   model   delta    sigma   weight residual
     111.28  101.66    9.62 1.09e+00 8.42e-01 7.79e+01
  angle pdb=" N   MET A 142 "
        pdb=" CA  MET A 142 "
        pdb=" C   MET A 142 "
      ideal   model   delta    sigma   weight residual
     111.28  101.67    9.61 1.09e+00 8.42e-01 7.77e+01
  ... (remaining 12568 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.37: 5447
       16.37 -    32.75: 171
       32.75 -    49.12: 23
       49.12 -    65.50: 19
       65.50 -    81.87: 10
  Dihedral angle restraints: 5670
    sinusoidal: 2088
      harmonic: 3582
  Sorted by residual:
  dihedral pdb=" CB  CYS A 389 "
           pdb=" SG  CYS A 389 "
           pdb=" SG  CYS A 412 "
           pdb=" CB  CYS A 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.87   81.87     1      1.00e+01 1.00e-02 8.24e+01
  dihedral pdb=" CB  CYS A 350 "
           pdb=" SG  CYS A 350 "
           pdb=" SG  CYS A 358 "
           pdb=" CB  CYS A 358 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.08   43.08     1      1.00e+01 1.00e-02 2.59e+01
  dihedral pdb=" CB  CYS A  66 "
           pdb=" SG  CYS A  66 "
           pdb=" SG  CYS A 187 "
           pdb=" CB  CYS A 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.49   31.49     1      1.00e+01 1.00e-02 1.41e+01
  ... (remaining 5667 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 940
       0.070 -    0.139: 466
       0.139 -    0.208: 118
       0.208 -    0.278: 30
       0.278 -    0.347: 9
  Chirality restraints: 1563
  Sorted by residual:
  chirality pdb=" C2  NAG B 602 "
            pdb=" C1  NAG B 602 "
            pdb=" C3  NAG B 602 "
            pdb=" N2  NAG B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.84    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" C2  NAG A 602 "
            pdb=" C1  NAG A 602 "
            pdb=" C3  NAG A 602 "
            pdb=" N2  NAG A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.84    0.35 2.00e-01 2.50e+01 3.00e+00
  chirality pdb=" C2  NAG C 602 "
            pdb=" C1  NAG C 602 "
            pdb=" C3  NAG C 602 "
            pdb=" N2  NAG C 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.84    0.35 2.00e-01 2.50e+01 2.99e+00
  ... (remaining 1560 not shown)

  Planarity restraints: 1620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  65 "    0.028 2.00e-02 2.50e+03   2.98e-02 1.11e+01
        pdb=" CG  ASN B  65 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  65 "   -0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  65 "   -0.047 2.00e-02 2.50e+03
        pdb=" C1  NAG B 601 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  65 "    0.028 2.00e-02 2.50e+03   2.97e-02 1.11e+01
        pdb=" CG  ASN A  65 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  65 "   -0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  65 "   -0.047 2.00e-02 2.50e+03
        pdb=" C1  NAG A 601 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C  65 "   -0.027 2.00e-02 2.50e+03   2.97e-02 1.10e+01
        pdb=" CG  ASN C  65 "    0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN C  65 "    0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN C  65 "    0.047 2.00e-02 2.50e+03
        pdb=" C1  NAG C 601 "   -0.036 2.00e-02 2.50e+03
  ... (remaining 1617 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 40
        2.60 -     3.17: 7716
        3.17 -     3.75: 12893
        3.75 -     4.32: 18017
        4.32 -     4.90: 29475
  Nonbonded interactions: 68141
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C 350 "
            pdb=" SG  CYS C 358 "
     model   vdw
     2.020 3.760
  nonbonded pdb=" SG  CYS B 350 "
            pdb=" SG  CYS B 358 "
     model   vdw
     2.020 3.760
  nonbonded pdb=" SG  CYS B 382 "
            pdb=" SG  CYS B 387 "
     model   vdw
     2.026 3.760
  nonbonded pdb=" SG  CYS C 382 "
            pdb=" SG  CYS C 387 "
     model   vdw
     2.026 3.760
  nonbonded pdb=" SG  CYS C 326 "
            pdb=" SG  CYS C 335 "
     model   vdw
     2.036 3.760
  ... (remaining 68136 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  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:             24.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     18.110
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
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      :  0.013   0.072   9216  Z= 0.841
  Angle     :  1.522  11.409  12573  Z= 1.074
  Chirality :  0.087   0.347   1563
  Planarity :  0.005   0.020   1614
  Dihedral  :  9.806  79.964   3345
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.33 %
    Favored  : 99.34 %
  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:  0.30 (0.21), residues: 1209
  helix:  0.53 (0.20), residues: 504
  sheet:  0.73 (0.40), residues: 159
  loop : -0.14 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.005   TRP A 303 
 HIS   0.002   0.001   HIS C 253 
 PHE   0.016   0.004   PHE B 230 
 TYR   0.027   0.005   TYR B 202 
 ARG   0.004   0.001   ARG C 314 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.984 
Fit side-chains
REVERT: B  217 VAL cc_start: 0.9116 (t) cc_final: 0.8912 (m)
REVERT: B  404 VAL cc_start: 0.8501 (t) cc_final: 0.8275 (t)
REVERT: B  473 GLU cc_start: 0.7893 (tt0) cc_final: 0.7653 (tt0)
REVERT: C  463 GLN cc_start: 0.7851 (mm110) cc_final: 0.7644 (mm110)
  outliers start: 3
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2625
  time to fit residues: 54.6320
Evaluate side-chains
  85 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 1.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.5980
   chunk 90 optimal weight:    0.5980
   chunk 50 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0170
   chunk 61 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 94 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 70 optimal weight:    0.3980
   chunk 108 optimal weight:    0.8980
   overall best weight:    0.3218

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN
A 352 GLN
B  95 ASN
B 352 GLN
C  95 ASN
C 279 ASN
C 352 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.160344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.152190 restraints weight = 11300.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.139070 restraints weight = 18955.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.138877 restraints weight = 14914.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9216  Z= 0.216
  Angle     :  0.599   6.488  12573  Z= 0.333
  Chirality :  0.045   0.141   1563
  Planarity :  0.004   0.028   1614
  Dihedral  :  4.877  20.310   1431
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  6.42 %
    Favored  : 91.14 %
  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:  1.64 (0.23), residues: 1209
  helix:  2.61 (0.23), residues: 510
  sheet:  0.62 (0.39), residues: 150
  loop : -0.24 (0.22), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 303 
 HIS   0.001   0.000   HIS C  24 
 PHE   0.013   0.002   PHE C 209 
 TYR   0.018   0.002   TYR C 427 
 ARG   0.004   0.001   ARG C 232 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.966 
Fit side-chains
REVERT: B  217 VAL cc_start: 0.9074 (t) cc_final: 0.8816 (m)
REVERT: C  427 TYR cc_start: 0.8344 (t80) cc_final: 0.8094 (t80)
  outliers start: 22
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1910
  time to fit residues: 29.4470
Evaluate side-chains
  77 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain C residue  266 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0770
   chunk 36 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0050
   chunk 21 optimal weight:    0.0870
   chunk 119 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.3130

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.136349 restraints weight = 11339.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.136267 restraints weight = 10544.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.136267 restraints weight = 10987.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9216  Z= 0.189
  Angle     :  0.520   5.652  12573  Z= 0.285
  Chirality :  0.044   0.140   1563
  Planarity :  0.003   0.035   1614
  Dihedral  :  4.252  18.055   1431
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  :  7.75 %
    Favored  : 88.93 %
  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:  1.98 (0.24), residues: 1209
  helix:  3.13 (0.24), residues: 510
  sheet:  0.76 (0.40), residues: 150
  loop : -0.31 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 303 
 HIS   0.001   0.000   HIS C  24 
 PHE   0.008   0.001   PHE B 277 
 TYR   0.015   0.001   TYR C 427 
 ARG   0.003   0.000   ARG C 388 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.982 
Fit side-chains
REVERT: B  217 VAL cc_start: 0.9128 (t) cc_final: 0.8798 (m)
REVERT: B  388 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7931 (mtm-85)
REVERT: B  467 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7150 (t0)
REVERT: C  427 TYR cc_start: 0.8174 (t80) cc_final: 0.7795 (t80)
  outliers start: 30
  outliers final: 16
  residues processed: 104
  average time/residue: 0.2004
  time to fit residues: 30.0072
Evaluate side-chains
  83 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  467 ASP
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 116 optimal weight:    2.9990
   chunk 73 optimal weight:    0.4980
   chunk 113 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.139802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.118960 restraints weight = 11435.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.119043 restraints weight = 10813.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.119060 restraints weight = 10423.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9216  Z= 0.346
  Angle     :  0.600   7.225  12573  Z= 0.325
  Chirality :  0.047   0.186   1563
  Planarity :  0.004   0.039   1614
  Dihedral  :  4.408  18.068   1431
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  :  9.19 %
    Favored  : 86.49 %
  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:  1.53 (0.23), residues: 1209
  helix:  2.68 (0.23), residues: 513
  sheet:  0.57 (0.42), residues: 150
  loop : -0.51 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 303 
 HIS   0.003   0.001   HIS B 253 
 PHE   0.010   0.002   PHE B 310 
 TYR   0.022   0.002   TYR A 427 
 ARG   0.002   0.000   ARG B 388 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 73
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7154 (tt)
REVERT: C  184 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7389 (tm-30)
REVERT: C  233 ASN cc_start: 0.8842 (t0) cc_final: 0.8532 (t0)
REVERT: C  424 VAL cc_start: 0.8206 (t) cc_final: 0.7990 (p)
REVERT: C  467 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7332 (t0)
  outliers start: 39
  outliers final: 24
  residues processed: 107
  average time/residue: 0.1711
  time to fit residues: 27.9200
Evaluate side-chains
  95 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 69
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Chi-restraints excluded: chain C residue  432 GLU
Chi-restraints excluded: chain C residue  467 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0000
   chunk 82 optimal weight:    0.5980
   chunk 108 optimal weight:    0.1980
   chunk 45 optimal weight:    0.2980
   chunk 94 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 114 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.3784

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

Flipped N/Q/H residues before XYZ refinement:
C 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.140472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.116253 restraints weight = 11339.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.117845 restraints weight = 9226.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.118765 restraints weight = 7911.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9216  Z= 0.198
  Angle     :  0.509   7.659  12573  Z= 0.272
  Chirality :  0.044   0.141   1563
  Planarity :  0.004   0.045   1614
  Dihedral  :  4.199  17.468   1431
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 11.18 %
    Favored  : 85.71 %
  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 (0.24), residues: 1209
  helix:  3.00 (0.24), residues: 516
  sheet:  0.60 (0.44), residues: 150
  loop : -0.56 (0.23), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 303 
 HIS   0.001   0.001   HIS C  24 
 PHE   0.008   0.001   PHE C 230 
 TYR   0.012   0.001   TYR A 345 
 ARG   0.002   0.000   ARG B 388 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  388 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.7957 (mtm-85)
REVERT: C  424 VAL cc_start: 0.8228 (t) cc_final: 0.7961 (p)
  outliers start: 28
  outliers final: 17
  residues processed: 98
  average time/residue: 0.2021
  time to fit residues: 28.6586
Evaluate side-chains
  84 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 116 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 50 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 83 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.140619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.118758 restraints weight = 11445.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.119910 restraints weight = 10416.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.120365 restraints weight = 9343.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9216  Z= 0.282
  Angle     :  0.554   8.911  12573  Z= 0.294
  Chirality :  0.045   0.163   1563
  Planarity :  0.004   0.042   1614
  Dihedral  :  4.232  17.260   1431
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 12.74 %
    Favored  : 83.72 %
  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:  1.59 (0.24), residues: 1209
  helix:  2.90 (0.23), residues: 516
  sheet:  0.70 (0.46), residues: 144
  loop : -0.70 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 303 
 HIS   0.002   0.001   HIS B 253 
 PHE   0.009   0.001   PHE B 277 
 TYR   0.017   0.002   TYR B 427 
 ARG   0.002   0.000   ARG B 388 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 74
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: B  233 ASN cc_start: 0.8742 (t0) cc_final: 0.8499 (t0)
REVERT: C  233 ASN cc_start: 0.8872 (t0) cc_final: 0.8638 (t0)
  outliers start: 32
  outliers final: 23
  residues processed: 101
  average time/residue: 0.2196
  time to fit residues: 31.3677
Evaluate side-chains
  88 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Chi-restraints excluded: chain C residue  389 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   chunk 86 optimal weight:    0.3980
   chunk 6 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0980
   chunk 63 optimal weight:    0.4980
   chunk 87 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.141770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.119911 restraints weight = 11647.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.120478 restraints weight = 10363.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.121451 restraints weight = 9518.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9216  Z= 0.226
  Angle     :  0.523   9.104  12573  Z= 0.276
  Chirality :  0.044   0.163   1563
  Planarity :  0.004   0.044   1614
  Dihedral  :  4.163  17.081   1431
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.98 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 13.51 %
    Favored  : 83.39 %
  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:  1.61 (0.25), residues: 1209
  helix:  3.03 (0.24), residues: 516
  sheet:  0.66 (0.47), residues: 144
  loop : -0.82 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 303 
 HIS   0.001   0.001   HIS B 253 
 PHE   0.008   0.001   PHE B 277 
 TYR   0.031   0.002   TYR C 427 
 ARG   0.001   0.000   ARG C 309 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
REVERT: C  233 ASN cc_start: 0.8862 (t0) cc_final: 0.8633 (t0)
REVERT: C  446 ILE cc_start: 0.8293 (mm) cc_final: 0.7892 (mt)
  outliers start: 28
  outliers final: 24
  residues processed: 93
  average time/residue: 0.1691
  time to fit residues: 24.1863
Evaluate side-chains
  86 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Chi-restraints excluded: chain C residue  389 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 84 optimal weight:    0.0970
   chunk 24 optimal weight:    0.6980
   chunk 99 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0980
   chunk 113 optimal weight:    4.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.4578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.142115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.130377 restraints weight = 11855.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.118279 restraints weight = 20495.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.119666 restraints weight = 16653.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9216  Z= 0.225
  Angle     :  0.527   8.628  12573  Z= 0.278
  Chirality :  0.044   0.157   1563
  Planarity :  0.004   0.043   1614
  Dihedral  :  4.131  16.843   1431
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.31 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.51 %
    Favored  : 82.61 %
  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:  1.58 (0.25), residues: 1209
  helix:  3.07 (0.23), residues: 516
  sheet:  0.62 (0.47), residues: 144
  loop : -0.90 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 303 
 HIS   0.001   0.001   HIS B 253 
 PHE   0.008   0.001   PHE B 277 
 TYR   0.022   0.002   TYR B 427 
 ARG   0.002   0.000   ARG C 388 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
REVERT: B  233 ASN cc_start: 0.8745 (t0) cc_final: 0.8534 (t0)
REVERT: C  233 ASN cc_start: 0.8920 (t0) cc_final: 0.8688 (t0)
REVERT: C  446 ILE cc_start: 0.8335 (mm) cc_final: 0.7938 (mt)
  outliers start: 26
  outliers final: 24
  residues processed: 91
  average time/residue: 0.1831
  time to fit residues: 25.4992
Evaluate side-chains
  89 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 65
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0060
   chunk 116 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 41 optimal weight:    0.1980
   chunk 103 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.3196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.144027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 102)---------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.126513 restraints weight = 11643.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.123932 restraints weight = 22505.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.124628 restraints weight = 21039.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9216  Z= 0.178
  Angle     :  0.513  11.756  12573  Z= 0.266
  Chirality :  0.043   0.152   1563
  Planarity :  0.004   0.043   1614
  Dihedral  :  4.039  16.977   1431
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.06 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.39 %
    Favored  : 82.28 %
  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:  1.70 (0.25), residues: 1209
  helix:  3.21 (0.24), residues: 516
  sheet:  0.67 (0.47), residues: 144
  loop : -0.88 (0.24), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 303 
 HIS   0.001   0.000   HIS A  24 
 PHE   0.008   0.001   PHE C 230 
 TYR   0.017   0.001   TYR C 345 
 ARG   0.001   0.000   ARG A 232 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
REVERT: C  446 ILE cc_start: 0.8346 (mm) cc_final: 0.7934 (mt)
  outliers start: 21
  outliers final: 17
  residues processed: 92
  average time/residue: 0.1893
  time to fit residues: 26.7611
Evaluate side-chains
  79 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 63 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0980
   chunk 17 optimal weight:    0.0970
   chunk 42 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
C 279 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.142596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.133763 restraints weight = 11703.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.120311 restraints weight = 22248.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.120361 restraints weight = 17696.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.4462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9216  Z= 0.212
  Angle     :  0.528  11.229  12573  Z= 0.274
  Chirality :  0.044   0.157   1563
  Planarity :  0.004   0.044   1614
  Dihedral  :  4.029  16.850   1431
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.14 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.61 %
    Favored  : 81.62 %
  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:  1.63 (0.25), residues: 1209
  helix:  3.15 (0.23), residues: 516
  sheet:  0.66 (0.48), residues: 144
  loop : -0.92 (0.24), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 303 
 HIS   0.001   0.000   HIS B 253 
 PHE   0.008   0.001   PHE B 277 
 TYR   0.024   0.002   TYR A 427 
 ARG   0.001   0.000   ARG A 314 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8645 (m110)
REVERT: C  446 ILE cc_start: 0.8336 (mm) cc_final: 0.7938 (mt)
  outliers start: 25
  outliers final: 21
  residues processed: 88
  average time/residue: 0.1646
  time to fit residues: 22.6314
Evaluate side-chains
  84 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  279 ASN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Chi-restraints excluded: chain C residue  389 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 29 optimal weight:    0.0020
   chunk 67 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 118 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.141764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.121348 restraints weight = 11624.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.119336 restraints weight = 15060.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.119866 restraints weight = 14635.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.337   9216  Z= 0.407
  Angle     :  0.919  59.200  12573  Z= 0.526
  Chirality :  0.050   0.857   1563
  Planarity :  0.004   0.048   1614
  Dihedral  :  4.033  16.827   1431
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.23 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.84 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.26 %
  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:  1.63 (0.25), residues: 1209
  helix:  3.13 (0.23), residues: 516
  sheet:  0.92 (0.48), residues: 138
  loop : -0.95 (0.23), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 303 
 HIS   0.001   0.000   HIS B 253 
 PHE   0.009   0.001   PHE B 277 
 TYR   0.031   0.002   TYR A 379 
 ARG   0.001   0.000   ARG C 232 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2772.66 seconds
wall clock time: 51 minutes 41.63 seconds (3101.63 seconds total)