Starting phenix.real_space_refine
on Thu Mar 13 18:44:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tve_41639/03_2025/8tve_41639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tve_41639/03_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_41639/03_2025/8tve_41639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tve_41639/03_2025/8tve_41639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tve_41639/03_2025/8tve_41639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tve_41639/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.46, per 1000 atoms: 0.82
  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=15, 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
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 187 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 187 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C 326 " - pdb=" SG  CYS C 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 326 " - pdb=" SG  CYS B 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 350 " - pdb=" SG  CYS C 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 382 " - pdb=" SG  CYS C 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 389 " - pdb=" SG  CYS C 412 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 389 " - pdb=" SG  CYS B 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: 2.25
  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: 1.20
  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: 2.96

  Time building geometry restraints manager: 2.68 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 -    16.38: 5451
       16.38 -    32.75: 183
       32.75 -    49.13: 33
       49.13 -    65.50: 21
       65.50 -    81.88: 12
  Dihedral angle restraints: 5700
    sinusoidal: 2118
      harmonic: 3582
  Sorted by residual:
  dihedral pdb=" CB  CYS B 389 "
           pdb=" SG  CYS B 389 "
           pdb=" SG  CYS B 412 "
           pdb=" CB  CYS B 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.88   81.88     1      1.00e+01 1.00e-02 8.24e+01
  dihedral pdb=" CB  CYS C 389 "
           pdb=" SG  CYS C 389 "
           pdb=" SG  CYS C 412 "
           pdb=" CB  CYS C 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 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
  ... (remaining 5697 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:
        2.43 -     2.93: 3860
        2.93 -     3.42: 8456
        3.42 -     3.91: 14542
        3.91 -     4.41: 15317
        4.41 -     4.90: 25936
  Nonbonded interactions: 68111
  Sorted by model distance:
  nonbonded pdb=" N   THR B 392 "
            pdb=" N   ASP B 393 "
     model   vdw
     2.433 2.560
  nonbonded pdb=" N   THR C 392 "
            pdb=" N   ASP C 393 "
     model   vdw
     2.433 2.560
  nonbonded pdb=" N   THR A 392 "
            pdb=" N   ASP A 393 "
     model   vdw
     2.433 2.560
  nonbonded pdb=" N   SER B 356 "
            pdb=" O   SER B 356 "
     model   vdw
     2.513 2.496
  nonbonded pdb=" N   SER C 356 "
            pdb=" O   SER C 356 "
     model   vdw
     2.513 2.496
  ... (remaining 68106 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:             85.090
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.460
  Find NCS groups from input model:        0.170
  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:             0.010
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  115.260
-------------------------------------------------------------------------------
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= 0.828
  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 : 2.433

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  : 0.946 
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: 0.2746
  time to fit residues: 57.2938
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  : 1.183 
-------------------------------------------------------------------------------
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:    0.9990
   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 352 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.148303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.125487 restraints weight = 11214.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125965 restraints weight = 11881.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.127383 restraints weight = 9583.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9216  Z= 0.211
  Angle     :  0.587   6.329  12573  Z= 0.325
  Chirality :  0.045   0.138   1563
  Planarity :  0.004   0.029   1614
  Dihedral  :  4.843  18.982   1431
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  7.09 %
    Favored  : 90.70 %
  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:  1.62 (0.23), residues: 1209
  helix:  2.65 (0.23), residues: 510
  sheet:  0.59 (0.39), residues: 150
  loop : -0.30 (0.22), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 303 
 HIS   0.000   0.000   HIS C 253 
 PHE   0.011   0.002   PHE C 209 
 TYR   0.020   0.002   TYR C 427 
 ARG   0.003   0.001   ARG A 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
  112 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 1.193 
Fit side-chains
REVERT: B  217 VAL cc_start: 0.9052 (t) cc_final: 0.8786 (m)
REVERT: B  447 ASP cc_start: 0.8095 (m-30) cc_final: 0.7861 (m-30)
REVERT: C  427 TYR cc_start: 0.8327 (t80) cc_final: 0.8067 (t80)
  outliers start: 20
  outliers final: 9
  residues processed: 105
  average time/residue: 0.2118
  time to fit residues: 33.3194
Evaluate side-chains
  73 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
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  190 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
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:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 21 optimal weight:    0.1980
   chunk 119 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.141868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.119900 restraints weight = 11478.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.121417 restraints weight = 10498.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.121995 restraints weight = 9098.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9216  Z= 0.301
  Angle     :  0.585   6.603  12573  Z= 0.321
  Chirality :  0.046   0.145   1563
  Planarity :  0.004   0.035   1614
  Dihedral  :  4.436  17.759   1431
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  :  7.86 %
    Favored  : 88.26 %
  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 (0.23), residues: 1209
  helix:  2.75 (0.23), residues: 513
  sheet:  0.58 (0.41), residues: 150
  loop : -0.48 (0.22), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 303 
 HIS   0.003   0.001   HIS B 253 
 PHE   0.009   0.002   PHE A 310 
 TYR   0.017   0.002   TYR C 427 
 ARG   0.002   0.000   ARG A 360 

*********************** 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
  109 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 74
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
REVERT: A  233 ASN cc_start: 0.8641 (t0) cc_final: 0.8418 (t0)
REVERT: C  233 ASN cc_start: 0.8771 (t0) cc_final: 0.8466 (t0)
REVERT: C  427 TYR cc_start: 0.8282 (t80) cc_final: 0.7759 (t80)
  outliers start: 35
  outliers final: 22
  residues processed: 106
  average time/residue: 0.1978
  time to fit residues: 30.0280
Evaluate side-chains
  86 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
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  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  153 VAL
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  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  363 VAL
Chi-restraints excluded: chain B residue  432 GLU
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  190 ILE
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:    0.0670
   chunk 24 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 116 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 83 optimal weight:    0.3980
   chunk 90 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.141614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.121009 restraints weight = 11413.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.120026 restraints weight = 12258.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.120267 restraints weight = 12353.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9216  Z= 0.270
  Angle     :  0.544   6.960  12573  Z= 0.294
  Chirality :  0.045   0.140   1563
  Planarity :  0.004   0.041   1614
  Dihedral  :  4.353  17.623   1431
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  :  8.53 %
    Favored  : 88.04 %
  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:  1.54 (0.24), residues: 1209
  helix:  2.79 (0.23), residues: 513
  sheet:  0.45 (0.43), residues: 150
  loop : -0.57 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 303 
 HIS   0.002   0.001   HIS B 253 
 PHE   0.008   0.002   PHE C 277 
 TYR   0.022   0.002   TYR B 427 
 ARG   0.002   0.000   ARG A 232 

*********************** 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
  103 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  233 ASN cc_start: 0.8802 (t0) cc_final: 0.8532 (t0)
  outliers start: 31
  outliers final: 18
  residues processed: 101
  average time/residue: 0.2029
  time to fit residues: 31.4518
Evaluate side-chains
  80 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 2.806 
-------------------------------------------------------------------------------
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  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  153 VAL
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  215 ASN
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  432 GLU
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 107 optimal weight:    0.2980
   chunk 62 optimal weight:    0.0970
   chunk 82 optimal weight:    0.6980
   chunk 108 optimal weight:    0.8980
   chunk 45 optimal weight:    0.1980
   chunk 94 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.144185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.133979 restraints weight = 11415.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120775 restraints weight = 23735.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.122049 restraints weight = 18580.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9216  Z= 0.200
  Angle     :  0.513   7.345  12573  Z= 0.272
  Chirality :  0.044   0.176   1563
  Planarity :  0.004   0.041   1614
  Dihedral  :  4.185  17.343   1431
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 10.85 %
    Favored  : 85.60 %
  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 (0.24), residues: 1209
  helix:  3.03 (0.24), residues: 516
  sheet:  0.72 (0.45), residues: 144
  loop : -0.55 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 303 
 HIS   0.001   0.000   HIS C  24 
 PHE   0.007   0.001   PHE A 277 
 TYR   0.017   0.001   TYR A 427 
 ARG   0.003   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
  100 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 68
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  233 ASN cc_start: 0.8842 (t0) cc_final: 0.8615 (t0)
REVERT: C  446 ILE cc_start: 0.8353 (mm) cc_final: 0.7957 (mt)
  outliers start: 32
  outliers final: 21
  residues processed: 95
  average time/residue: 0.1632
  time to fit residues: 24.2190
Evaluate side-chains
  83 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  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  469 ILE
Chi-restraints excluded: chain B residue  153 VAL
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  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue  158 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 116 optimal weight:    0.7980
   chunk 56 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.3980
   chunk 83 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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**
A 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.140993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.119532 restraints weight = 11384.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.119591 restraints weight = 10274.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.119685 restraints weight = 10961.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9216  Z= 0.265
  Angle     :  0.544   9.387  12573  Z= 0.288
  Chirality :  0.044   0.146   1563
  Planarity :  0.004   0.040   1614
  Dihedral  :  4.215  17.146   1431
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 12.29 %
    Favored  : 83.83 %
  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:  1.56 (0.24), residues: 1209
  helix:  2.91 (0.23), residues: 516
  sheet:  0.67 (0.46), residues: 144
  loop : -0.76 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 303 
 HIS   0.002   0.001   HIS B 253 
 PHE   0.008   0.001   PHE C 277 
 TYR   0.018   0.002   TYR A 427 
 ARG   0.001   0.000   ARG C 258 

*********************** 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
  105 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 70
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LEU cc_start: 0.8730 (tp) cc_final: 0.8485 (tp)
REVERT: B  233 ASN cc_start: 0.8787 (t0) cc_final: 0.8535 (t0)
REVERT: C  233 ASN cc_start: 0.8930 (t0) cc_final: 0.8670 (t0)
  outliers start: 35
  outliers final: 31
  residues processed: 99
  average time/residue: 0.1946
  time to fit residues: 27.9220
Evaluate side-chains
  95 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 64
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
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  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  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  153 VAL
Chi-restraints excluded: chain B residue  158 LEU
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  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  185 LEU
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  348 ILE
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 91 optimal weight:    0.2980
   chunk 86 optimal weight:    0.2980
   chunk 6 optimal weight:    0.3980
   chunk 70 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 98 optimal weight:    0.1980
   chunk 89 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3614 r_free = 0.3614 target = 0.142719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.123151 restraints weight = 11569.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.123066 restraints weight = 11660.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.123074 restraints weight = 10842.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.4093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9216  Z= 0.215
  Angle     :  0.540  11.978  12573  Z= 0.282
  Chirality :  0.044   0.221   1563
  Planarity :  0.004   0.042   1614
  Dihedral  :  4.168  16.995   1431
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 13.51 %
    Favored  : 83.28 %
  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:  1.67 (0.24), residues: 1209
  helix:  3.05 (0.23), residues: 516
  sheet:  0.72 (0.47), residues: 144
  loop : -0.75 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 303 
 HIS   0.001   0.000   HIS B 253 
 PHE   0.008   0.001   PHE C 277 
 TYR   0.021   0.002   TYR A 427 
 ARG   0.002   0.000   ARG B 220 

*********************** 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
  100 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 71
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LEU cc_start: 0.8742 (tp) cc_final: 0.8501 (tp)
REVERT: C  233 ASN cc_start: 0.8880 (t0) cc_final: 0.8635 (t0)
REVERT: C  345 TYR cc_start: 0.7230 (t80) cc_final: 0.6965 (t80)
REVERT: C  446 ILE cc_start: 0.8293 (mm) cc_final: 0.7900 (mt)
  outliers start: 29
  outliers final: 26
  residues processed: 96
  average time/residue: 0.1776
  time to fit residues: 25.3529
Evaluate side-chains
  89 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 63
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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  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  469 ILE
Chi-restraints excluded: chain B residue  153 VAL
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 B residue  348 ILE
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  158 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0670
   chunk 93 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 43 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0980
   chunk 113 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.3918

-------------------------------------------------------------------------------
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 = 0.143643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.123741 restraints weight = 11790.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.123674 restraints weight = 11650.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.123853 restraints weight = 11011.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.4278

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= 0.200
  Angle     :  0.520   9.130  12573  Z= 0.272
  Chirality :  0.044   0.160   1563
  Planarity :  0.004   0.043   1614
  Dihedral  :  4.079  16.703   1431
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 13.51 %
    Favored  : 83.06 %
  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:  3.13 (0.23), residues: 516
  sheet:  0.71 (0.48), residues: 144
  loop : -0.80 (0.23), residues: 549

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   0.007   0.001   PHE C 277 
 TYR   0.021   0.001   TYR B 427 
 ARG   0.001   0.000   ARG A 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
  100 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 69
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LEU cc_start: 0.8751 (tp) cc_final: 0.8511 (tp)
REVERT: C  185 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7043 (tt)
REVERT: C  233 ASN cc_start: 0.8927 (t0) cc_final: 0.8667 (t0)
REVERT: C  446 ILE cc_start: 0.8310 (mm) cc_final: 0.7917 (mt)
  outliers start: 31
  outliers final: 26
  residues processed: 96
  average time/residue: 0.2096
  time to fit residues: 31.8437
Evaluate side-chains
  89 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 62
  time to evaluate  : 2.511 
-------------------------------------------------------------------------------
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  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  298 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  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  298 VAL
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  185 LEU
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  348 ILE
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:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 116 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0060
   chunk 28 optimal weight:    0.7980
   chunk 41 optimal weight:    0.2980
   chunk 103 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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 = 0.3611 r_free = 0.3611 target = 0.142783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.123027 restraints weight = 11669.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.123216 restraints weight = 11211.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.123217 restraints weight = 10785.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9216  Z= 0.225
  Angle     :  0.534   8.787  12573  Z= 0.278
  Chirality :  0.044   0.162   1563
  Planarity :  0.004   0.041   1614
  Dihedral  :  4.084  17.001   1431
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.62 %
    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:  1.63 (0.25), residues: 1209
  helix:  3.10 (0.23), residues: 516
  sheet:  0.67 (0.48), residues: 144
  loop : -0.85 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 303 
 HIS   0.001   0.000   HIS A 253 
 PHE   0.008   0.001   PHE C 277 
 TYR   0.032   0.002   TYR C 427 
 ARG   0.003   0.000   ARG C 388 

*********************** 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
  92 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 64
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  233 ASN cc_start: 0.8937 (t0) cc_final: 0.8681 (t0)
REVERT: C  446 ILE cc_start: 0.8314 (mm) cc_final: 0.7906 (mt)
  outliers start: 28
  outliers final: 26
  residues processed: 88
  average time/residue: 0.2401
  time to fit residues: 33.2820
Evaluate side-chains
  87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
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  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  298 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  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  298 VAL
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
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  348 ILE
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:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0980
   chunk 45 optimal weight:    0.5980
   chunk 95 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 17 optimal weight:    0.0270
   chunk 42 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.3238

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.143982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.124210 restraints weight = 11653.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.123801 restraints weight = 12235.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.123777 restraints weight = 11992.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.4432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9216  Z= 0.183
  Angle     :  0.562  10.630  12573  Z= 0.289
  Chirality :  0.045   0.211   1563
  Planarity :  0.004   0.046   1614
  Dihedral  :  4.082  16.836   1431
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 14.95 %
    Favored  : 81.84 %
  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:  1.71 (0.25), residues: 1209
  helix:  3.16 (0.23), residues: 513
  sheet:  0.70 (0.48), residues: 144
  loop : -0.78 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 303 
 HIS   0.000   0.000   HIS A  24 
 PHE   0.007   0.001   PHE C 230 
 TYR   0.022   0.001   TYR B 427 
 ARG   0.003   0.000   ARG B  64 

********************** 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
  91 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 62
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  233 ASN cc_start: 0.8919 (t0) cc_final: 0.8643 (t0)
REVERT: C  446 ILE cc_start: 0.8316 (mm) cc_final: 0.7931 (mt)
  outliers start: 29
  outliers final: 26
  residues processed: 87
  average time/residue: 0.2213
  time to fit residues: 29.8458
Evaluate side-chains
  85 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 59
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 CYS
Chi-restraints excluded: chain A residue  167 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  298 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   66 CYS
Chi-restraints excluded: chain B residue  166 VAL
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  298 VAL
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
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  348 ILE
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 29 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0010
   chunk 90 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0370
   chunk 62 optimal weight:    0.6980
   chunk 118 optimal weight:    0.0040
   chunk 82 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0970
   chunk 117 optimal weight:    0.0670
   chunk 72 optimal weight:    0.0670
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.0352

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.150830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.141459 restraints weight = 11551.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.131568 restraints weight = 21033.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.129734 restraints weight = 18927.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.4695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9216  Z= 0.127
  Angle     :  0.525  10.231  12573  Z= 0.268
  Chirality :  0.043   0.142   1563
  Planarity :  0.004   0.046   1614
  Dihedral  :  3.848  16.978   1431
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.61 %
    Favored  : 81.84 %
  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:  1.89 (0.25), residues: 1209
  helix:  3.31 (0.23), residues: 516
  sheet:  0.85 (0.48), residues: 144
  loop : -0.73 (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 A 253 
 PHE   0.011   0.001   PHE C 230 
 TYR   0.021   0.001   TYR A 427 
 ARG   0.001   0.000   ARG C 220 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3089.32 seconds
wall clock time: 57 minutes 7.76 seconds (3427.76 seconds total)