Starting phenix.real_space_refine
on Wed Mar 12 06:05:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uqk_42472/03_2025/8uqk_42472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uqk_42472/03_2025/8uqk_42472.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uqk_42472/03_2025/8uqk_42472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uqk_42472/03_2025/8uqk_42472.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uqk_42472/03_2025/8uqk_42472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uqk_42472/03_2025/8uqk_42472.cif"
  }
  resolution = 4.61
  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=   0.009
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      18      5.16       5
     C    4630      2.51       5
     N    1332      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7318
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3659
          Classifications: {'peptide': 481}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 445}
    Chain: "A"
      Number of atoms: 3659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3659
          Classifications: {'peptide': 481}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 445}
  Time building chain proxies: 4.87, per 1000 atoms: 0.67
  Number of scatterers: 7318
  At special positions: 0
  Unit cell: (78.07, 114.995, 121.325, 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      18     16.00
     O    1338      8.00
     N    1332      7.00
     C    4630      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.80
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 6 sheets defined
      42.5% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 21
    Processing helix  chain 'B' and resid 44 through 52
      removed outlier: 3.717A  pdb=" N   GLN B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA B  49 " --> pdb=" O   ALA B  45 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LEU B  50 " --> pdb=" O   ASN B  46 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU B  51 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 59
    Processing helix  chain 'B' and resid 62 through 67
      removed outlier: 3.658A  pdb=" N   VAL B  66 " --> pdb=" O   THR B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 73
    Processing helix  chain 'B' and resid 74 through 82
      removed outlier: 4.813A  pdb=" N   ALA B  80 " --> pdb=" O   GLU B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 130
      removed outlier: 4.016A  pdb=" N   ARG B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   SER B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 154
    Processing helix  chain 'B' and resid 194 through 204
    Processing helix  chain 'B' and resid 242 through 253
    Processing helix  chain 'B' and resid 283 through 319
      removed outlier: 3.560A  pdb=" N   CYS B 290 " --> pdb=" O   ARG B 286 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLU B 291 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   VAL B 292 " --> pdb=" O   ARG B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 327
    Processing helix  chain 'B' and resid 332 through 340
    Processing helix  chain 'B' and resid 340 through 349
      removed outlier: 3.549A  pdb=" N   VAL B 344 " --> pdb=" O   ASP B 340 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU B 346 " --> pdb=" O   ALA B 342 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   THR B 348 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 381
      removed outlier: 4.111A  pdb=" N   ALA B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 398
    Processing helix  chain 'B' and resid 399 through 402
    Processing helix  chain 'B' and resid 460 through 468
    Processing helix  chain 'B' and resid 475 through 481
      removed outlier: 3.513A  pdb=" N   LEU B 479 " --> pdb=" O   LYS B 475 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA B 481 " --> pdb=" O   ALA B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 487
      removed outlier: 3.508A  pdb=" N   PHE B 485 " --> pdb=" O   ALA B 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 21
    Processing helix  chain 'A' and resid 44 through 52
      removed outlier: 3.712A  pdb=" N   GLN A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ALA A  49 " --> pdb=" O   ALA A  45 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   LEU A  50 " --> pdb=" O   ASN A  46 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU A  51 " --> pdb=" O   THR A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 59
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 68 through 73
      removed outlier: 3.509A  pdb=" N   TRP A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 82
      removed outlier: 4.475A  pdb=" N   ALA A  80 " --> pdb=" O   GLU A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 130
      removed outlier: 3.578A  pdb=" N   SER A 130 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 154
      removed outlier: 3.828A  pdb=" N   LEU A 142 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA A 151 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 193
      removed outlier: 3.506A  pdb=" N   ASP A 192 " --> pdb=" O   PRO A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 204
    Processing helix  chain 'A' and resid 242 through 253
    Processing helix  chain 'A' and resid 283 through 319
      removed outlier: 3.540A  pdb=" N   ARG A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA A 289 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLU A 291 " --> pdb=" O   ARG A 287 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL A 292 " --> pdb=" O   ARG A 288 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A 294 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLN A 295 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 327
      removed outlier: 3.897A  pdb=" N   SER A 326 " --> pdb=" O   PRO A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 340
      removed outlier: 3.831A  pdb=" N   ASP A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 349
      removed outlier: 3.633A  pdb=" N   VAL A 344 " --> pdb=" O   ASP A 340 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLU A 346 " --> pdb=" O   ALA A 342 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   THR A 348 " --> pdb=" O   VAL A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 380
    Processing helix  chain 'A' and resid 393 through 398
    Processing helix  chain 'A' and resid 399 through 405
    Processing helix  chain 'A' and resid 460 through 468
    Processing helix  chain 'A' and resid 475 through 481
      removed outlier: 3.840A  pdb=" N   LEU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 487
      removed outlier: 3.770A  pdb=" N   PHE A 485 " --> pdb=" O   ALA A 481 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 33
      removed outlier: 3.563A  pdb=" N   THR B 104 " --> pdb=" O   PHE B  33 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 187 through 188
      removed outlier: 3.813A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   VAL B 160 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   GLU B 174 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   VAL B 158 " --> pdb=" O   GLU B 174 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU B 271 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   LEU B 268 " --> pdb=" O   LYS B 264 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LYS B 264 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 388 through 390
      removed outlier: 3.736A  pdb=" N   PHE B 389 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 33
      removed outlier: 3.974A  pdb=" N   VAL A  29 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU A 108 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE A  33 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A 104 " --> pdb=" O   PHE A  33 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 188
      removed outlier: 3.809A  pdb=" N   LEU A 172 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   VAL A 160 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   GLU A 174 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   VAL A 158 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LEU A 262 " --> pdb=" O   TRP A 269 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   LEU A 271 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU A 260 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ALA A 273 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   PHE A 258 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   HIS A 275 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ALA A 256 " --> pdb=" O   HIS A 275 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ARG A 207 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355
      removed outlier: 3.510A  pdb=" N   GLY A 352 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA A 354 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)

    283 hydrogen bonds defined for protein.
    783 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 2.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2519
        1.34 -     1.46: 1454
        1.46 -     1.58: 3479
        1.58 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 7482
  Sorted by residual:
  bond pdb=" N   PRO A  54 "
       pdb=" CA  PRO A  54 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.018 1.31e-02 5.83e+03 1.79e+00
  bond pdb=" N   VAL A 254 "
       pdb=" CA  VAL A 254 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.19e-02 7.06e+03 1.22e+00
  bond pdb=" CA  ASP A 116 "
       pdb=" CB  ASP A 116 "
    ideal  model  delta    sigma   weight residual
    1.527  1.545 -0.018 1.70e-02 3.46e+03 1.14e+00
  bond pdb=" N   VAL B 254 "
       pdb=" CA  VAL B 254 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.014 1.42e-02 4.96e+03 9.76e-01
  bond pdb=" C   VAL B 224 "
       pdb=" O   VAL B 224 "
    ideal  model  delta    sigma   weight residual
    1.232  1.241 -0.008 8.90e-03 1.26e+04 8.61e-01
  ... (remaining 7477 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 9975
        2.45 -     4.89: 197
        4.89 -     7.34: 21
        7.34 -     9.78: 1
        9.78 -    12.23: 2
  Bond angle restraints: 10196
  Sorted by residual:
  angle pdb=" N   GLY B 358 "
        pdb=" CA  GLY B 358 "
        pdb=" C   GLY B 358 "
      ideal   model   delta    sigma   weight residual
     114.25  109.51    4.74 1.30e+00 5.92e-01 1.33e+01
  angle pdb=" C   PRO A 115 "
        pdb=" N   ASP A 116 "
        pdb=" CA  ASP A 116 "
      ideal   model   delta    sigma   weight residual
     122.46  127.59   -5.13 1.41e+00 5.03e-01 1.33e+01
  angle pdb=" CA  LEU A 122 "
        pdb=" CB  LEU A 122 "
        pdb=" CG  LEU A 122 "
      ideal   model   delta    sigma   weight residual
     116.30  128.53  -12.23 3.50e+00 8.16e-02 1.22e+01
  angle pdb=" N   GLU A 123 "
        pdb=" CA  GLU A 123 "
        pdb=" C   GLU A 123 "
      ideal   model   delta    sigma   weight residual
     112.23  107.92    4.31 1.26e+00 6.30e-01 1.17e+01
  angle pdb=" N   ALA A  83 "
        pdb=" CA  ALA A  83 "
        pdb=" C   ALA A  83 "
      ideal   model   delta    sigma   weight residual
     108.46  113.37   -4.91 1.51e+00 4.39e-01 1.06e+01
  ... (remaining 10191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4115
       17.62 -    35.24: 364
       35.24 -    52.86: 44
       52.86 -    70.48: 11
       70.48 -    88.10: 8
  Dihedral angle restraints: 4542
    sinusoidal: 1792
      harmonic: 2750
  Sorted by residual:
  dihedral pdb=" CA  SER A 388 "
           pdb=" C   SER A 388 "
           pdb=" N   PHE A 389 "
           pdb=" CA  PHE A 389 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.13   22.87     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  ASP A 156 "
           pdb=" C   ASP A 156 "
           pdb=" N   ARG A 157 "
           pdb=" CA  ARG A 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.17  -20.83     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  ALA A  83 "
           pdb=" C   ALA A  83 "
           pdb=" N   LEU A  84 "
           pdb=" CA  LEU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.32   20.68     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 4539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 842
       0.038 -    0.076: 220
       0.076 -    0.113: 77
       0.113 -    0.151: 16
       0.151 -    0.189: 3
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" CG  LEU B 206 "
            pdb=" CB  LEU B 206 "
            pdb=" CD1 LEU B 206 "
            pdb=" CD2 LEU B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.92e-01
  chirality pdb=" CA  ASP A 116 "
            pdb=" N   ASP A 116 "
            pdb=" C   ASP A 116 "
            pdb=" CB  ASP A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.38e-01
  chirality pdb=" CA  ARG B 457 "
            pdb=" N   ARG B 457 "
            pdb=" C   ARG B 457 "
            pdb=" CB  ARG B 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.78e-01
  ... (remaining 1155 not shown)

  Planarity restraints: 1342
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 229 "   -0.041 5.00e-02 4.00e+02   6.25e-02 6.26e+00
        pdb=" N   PRO A 230 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 230 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 230 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  88 "   -0.032 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO B  89 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B  89 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  89 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  88 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.62e+00
        pdb=" N   PRO A  89 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A  89 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  89 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1339 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 463
        2.73 -     3.27: 8434
        3.27 -     3.81: 13029
        3.81 -     4.36: 15043
        4.36 -     4.90: 23143
  Nonbonded interactions: 60112
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 149 "
            pdb=" OG1 THR B 153 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   PRO A 322 "
            pdb=" OG1 THR A 325 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OE2 GLU A 312 "
            pdb=" NZ  LYS A 475 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   PRO B 456 "
            pdb=" N   GLY B 458 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O   SER A  44 "
            pdb=" OG1 THR A  47 "
     model   vdw
     2.234 3.040
  ... (remaining 60107 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
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:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.350
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7482  Z= 0.198
  Angle     :  0.862  12.226  10196  Z= 0.486
  Chirality :  0.040   0.189   1158
  Planarity :  0.006   0.063   1342
  Dihedral  : 13.606  88.100   2766
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 21.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.47 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.07 (0.25), residues: 958
  helix: -0.56 (0.27), residues: 304
  sheet: -1.72 (0.40), residues: 142
  loop : -1.77 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 379 
 HIS   0.006   0.001   HIS B 455 
 PHE   0.011   0.001   PHE A 385 
 TYR   0.012   0.002   TYR B  93 
 ARG   0.006   0.001   ARG B 404 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A   75 TRP cc_start: 0.9520 (t60) cc_final: 0.9203 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.2523
  time to fit residues: 11.4462
Evaluate side-chains
  20 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.3980
   chunk 72 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0970
   chunk 24 optimal weight:    4.9990
   chunk 49 optimal weight:    0.4980
   chunk 38 optimal weight:    8.9990
   chunk 75 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0570
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.3696
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.056319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.042987 restraints weight = 33941.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.044114 restraints weight = 25532.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.045051 restraints weight = 20386.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.6329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   7482  Z= 0.222
  Angle     :  0.802  11.587  10196  Z= 0.390
  Chirality :  0.045   0.179   1158
  Planarity :  0.006   0.071   1342
  Dihedral  :  5.670  21.381   1058
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.64 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -1.95 (0.25), residues: 958
  helix: -0.40 (0.28), residues: 312
  sheet: -0.80 (0.41), residues: 142
  loop : -2.06 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 455 
 PHE   0.007   0.001   PHE B 258 
 TYR   0.012   0.002   TYR B 284 
 ARG   0.030   0.001   ARG B 126 

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  268 LEU cc_start: 0.9220 (tp) cc_final: 0.8775 (tp)
REVERT: A  360 GLU cc_start: 0.9128 (pm20) cc_final: 0.8786 (pp20)
REVERT: A  401 LEU cc_start: 0.9685 (tp) cc_final: 0.9331 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1333
  time to fit residues: 7.4846
Evaluate side-chains
  23 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 68 optimal weight:    0.1980
   chunk 94 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0870
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 34 optimal weight:    9.9990
   chunk 91 optimal weight:    0.0970
   chunk 36 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.5758
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.056776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.043727 restraints weight = 35622.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.044923 restraints weight = 26330.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.045857 restraints weight = 20816.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start:          0.6747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7482  Z= 0.200
  Angle     :  0.749  12.263  10196  Z= 0.359
  Chirality :  0.042   0.150   1158
  Planarity :  0.006   0.049   1342
  Dihedral  :  5.320  23.200   1058
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.31 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.52 (0.25), residues: 958
  helix: -1.27 (0.26), residues: 332
  sheet: -0.79 (0.41), residues: 148
  loop : -2.27 (0.25), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 426 
 HIS   0.003   0.001   HIS B 451 
 PHE   0.007   0.001   PHE B  33 
 TYR   0.007   0.001   TYR B 398 
 ARG   0.014   0.001   ARG A 126 

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 MET cc_start: 0.8427 (tpp) cc_final: 0.8143 (tpp)
REVERT: A  360 GLU cc_start: 0.9049 (pm20) cc_final: 0.8713 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1134
  time to fit residues: 6.3661
Evaluate side-chains
  24 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 81 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0470
   chunk 51 optimal weight:    0.0040
   chunk 71 optimal weight:    3.9990
   chunk 55 optimal weight:    0.2980
   chunk 22 optimal weight:    6.9990
   chunk 47 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0070
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.0886
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.058039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.044970 restraints weight = 36028.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.046191 restraints weight = 26642.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.047055 restraints weight = 21043.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.7084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   7482  Z= 0.183
  Angle     :  0.737  11.526  10196  Z= 0.351
  Chirality :  0.042   0.164   1158
  Planarity :  0.005   0.040   1342
  Dihedral  :  5.164  22.287   1058
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.52 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.49 (0.25), residues: 958
  helix: -1.36 (0.26), residues: 342
  sheet: -0.55 (0.40), residues: 150
  loop : -2.25 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 426 
 HIS   0.004   0.001   HIS B 451 
 PHE   0.009   0.002   PHE B 258 
 TYR   0.027   0.002   TYR B 201 
 ARG   0.011   0.001   ARG A 126 

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8206 (t80) cc_final: 0.7079 (t80)
REVERT: A  260 LEU cc_start: 0.9047 (mm) cc_final: 0.8444 (mm)
REVERT: A  360 GLU cc_start: 0.9082 (pm20) cc_final: 0.8683 (pp20)
REVERT: A  362 LEU cc_start: 0.9295 (tt) cc_final: 0.8891 (mp)
REVERT: A  370 MET cc_start: 0.9698 (tpt) cc_final: 0.9493 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1129
  time to fit residues: 6.6470
Evaluate side-chains
  25 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 82 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0870
   chunk 58 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.5362
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.056275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.043288 restraints weight = 36147.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.044533 restraints weight = 26019.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.045421 restraints weight = 20223.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.7182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7482  Z= 0.189
  Angle     :  0.705  11.223  10196  Z= 0.342
  Chirality :  0.041   0.152   1158
  Planarity :  0.005   0.037   1342
  Dihedral  :  4.981  21.121   1058
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 17.60
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.52 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.65 (0.24), residues: 958
  helix: -1.53 (0.25), residues: 340
  sheet: -0.64 (0.40), residues: 150
  loop : -2.30 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 426 
 HIS   0.003   0.001   HIS B 451 
 PHE   0.010   0.001   PHE A 258 
 TYR   0.006   0.001   TYR B 398 
 ARG   0.008   0.001   ARG A 126 

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  117 MET cc_start: 0.9601 (mmp) cc_final: 0.9363 (mpp)
REVERT: A  258 PHE cc_start: 0.8202 (t80) cc_final: 0.7138 (t80)
REVERT: A  360 GLU cc_start: 0.9079 (pm20) cc_final: 0.8765 (mm-30)
REVERT: A  370 MET cc_start: 0.9719 (tpt) cc_final: 0.9461 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1156
  time to fit residues: 5.5197
Evaluate side-chains
  22 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   chunk 31 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0170
   chunk 36 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0030
   chunk 20 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0070
   overall best weight:    0.1646
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.057748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.044303 restraints weight = 35327.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.045622 restraints weight = 25467.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.046572 restraints weight = 19784.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.7420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7482  Z= 0.183
  Angle     :  0.749  10.000  10196  Z= 0.352
  Chirality :  0.042   0.160   1158
  Planarity :  0.005   0.039   1342
  Dihedral  :  4.964  20.666   1058
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.98 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.53 (0.25), residues: 958
  helix: -1.50 (0.25), residues: 344
  sheet: -0.43 (0.41), residues: 150
  loop : -2.23 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  75 
 HIS   0.005   0.001   HIS B 451 
 PHE   0.016   0.002   PHE A 258 
 TYR   0.009   0.001   TYR B 398 
 ARG   0.010   0.001   ARG B 126 

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8132 (t80) cc_final: 0.7243 (t80)
REVERT: A  360 GLU cc_start: 0.9053 (pm20) cc_final: 0.8762 (mm-30)
REVERT: A  370 MET cc_start: 0.9710 (tpt) cc_final: 0.9352 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1449
  time to fit residues: 6.6928
Evaluate side-chains
  26 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 0 optimal weight:   11.9990
   chunk 63 optimal weight:    0.0020
   chunk 86 optimal weight:    0.0060
   chunk 76 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 58 optimal weight:    0.2980
   chunk 81 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.3204
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.058248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.045127 restraints weight = 36012.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.046368 restraints weight = 26288.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.047306 restraints weight = 20654.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.7657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   7482  Z= 0.180
  Angle     :  0.724  10.102  10196  Z= 0.345
  Chirality :  0.042   0.172   1158
  Planarity :  0.005   0.040   1342
  Dihedral  :  4.810  22.154   1058
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.14 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.55 (0.24), residues: 958
  helix: -1.64 (0.25), residues: 346
  sheet: -0.25 (0.41), residues: 150
  loop : -2.22 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  75 
 HIS   0.004   0.001   HIS B 451 
 PHE   0.015   0.001   PHE A 258 
 TYR   0.013   0.002   TYR B 248 
 ARG   0.008   0.000   ARG A 126 

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8147 (t80) cc_final: 0.7246 (t80)
REVERT: A  360 GLU cc_start: 0.8998 (pm20) cc_final: 0.8729 (mm-30)
REVERT: A  370 MET cc_start: 0.9696 (tpt) cc_final: 0.9474 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1451
  time to fit residues: 7.1047
Evaluate side-chains
  27 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0980
   chunk 65 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0980
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0670
   chunk 91 optimal weight:    4.9990
   chunk 67 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    0.4520
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.058179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.045629 restraints weight = 38527.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.046792 restraints weight = 28118.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.047689 restraints weight = 22098.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.7725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7482  Z= 0.177
  Angle     :  0.717  10.483  10196  Z= 0.341
  Chirality :  0.041   0.165   1158
  Planarity :  0.006   0.054   1342
  Dihedral  :  4.825  21.386   1058
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.93 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.48 (0.25), residues: 958
  helix: -1.54 (0.25), residues: 346
  sheet: -0.21 (0.41), residues: 150
  loop : -2.21 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  75 
 HIS   0.004   0.001   HIS B 451 
 PHE   0.010   0.001   PHE A 258 
 TYR   0.016   0.002   TYR B 201 
 ARG   0.010   0.000   ARG B 126 

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8189 (t80) cc_final: 0.7279 (t80)
REVERT: A  360 GLU cc_start: 0.9048 (pm20) cc_final: 0.8791 (mm-30)
REVERT: A  370 MET cc_start: 0.9730 (tpt) cc_final: 0.9431 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1443
  time to fit residues: 6.9907
Evaluate side-chains
  26 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    0.0050
   chunk 4 optimal weight:    0.0970
   chunk 41 optimal weight:    0.9980
   chunk 65 optimal weight:    0.1980
   chunk 47 optimal weight:    9.9990
   chunk 17 optimal weight:    0.1980
   chunk 63 optimal weight:    0.3980
   chunk 66 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0970
   chunk 54 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0870
   overall best weight:    0.0968
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.058814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.046200 restraints weight = 37451.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.047454 restraints weight = 27251.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.048352 restraints weight = 21341.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
moved from start:          0.7903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7482  Z= 0.193
  Angle     :  0.741  10.098  10196  Z= 0.355
  Chirality :  0.042   0.156   1158
  Planarity :  0.005   0.041   1342
  Dihedral  :  4.812  20.963   1058
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.93 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.59 (0.25), residues: 958
  helix: -1.73 (0.24), residues: 346
  sheet: -0.56 (0.39), residues: 166
  loop : -2.11 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  75 
 HIS   0.005   0.001   HIS B 451 
 PHE   0.014   0.002   PHE B 389 
 TYR   0.011   0.002   TYR B 284 
 ARG   0.006   0.000   ARG B 126 

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 PHE cc_start: 0.8124 (t80) cc_final: 0.7204 (t80)
REVERT: A  370 MET cc_start: 0.9725 (tpt) cc_final: 0.9405 (tpt)
REVERT: A  411 LEU cc_start: 0.9265 (pt) cc_final: 0.8829 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1598
  time to fit residues: 7.7843
Evaluate side-chains
  27 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    0.0170
   chunk 61 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 83 optimal weight:    0.1980
   chunk 54 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 95 optimal weight:    9.9990
   chunk 80 optimal weight:    0.0170
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 39 optimal weight:    0.1980
   overall best weight:    0.2056
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.059375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.046836 restraints weight = 37302.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.048042 restraints weight = 27257.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.048965 restraints weight = 21443.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
moved from start:          0.8162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7482  Z= 0.186
  Angle     :  0.726   9.490  10196  Z= 0.347
  Chirality :  0.041   0.166   1158
  Planarity :  0.006   0.058   1342
  Dihedral  :  4.707  20.494   1058
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.72 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.37 (0.25), residues: 958
  helix: -1.56 (0.25), residues: 332
  sheet: -0.80 (0.38), residues: 176
  loop : -1.83 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 167 
 HIS   0.004   0.001   HIS B 451 
 PHE   0.009   0.001   PHE A 389 
 TYR   0.010   0.002   TYR B 248 
 ARG   0.011   0.001   ARG A 139 

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  188 PHE cc_start: 0.7569 (t80) cc_final: 0.7353 (t80)
REVERT: A  201 TYR cc_start: 0.8983 (m-80) cc_final: 0.8732 (m-80)
REVERT: A  258 PHE cc_start: 0.8039 (t80) cc_final: 0.7202 (t80)
REVERT: A  370 MET cc_start: 0.9663 (tpt) cc_final: 0.9436 (tpt)
REVERT: A  411 LEU cc_start: 0.9266 (pt) cc_final: 0.8808 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1541
  time to fit residues: 7.1118
Evaluate side-chains
  25 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 58 optimal weight:    0.3980
   chunk 66 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0370
   chunk 49 optimal weight:    0.4980
   chunk 17 optimal weight:    0.2980
   chunk 13 optimal weight:    5.9990
   chunk 53 optimal weight:    0.3980
   chunk 46 optimal weight:    0.4980
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.3258
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.058985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.046667 restraints weight = 36654.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.047872 restraints weight = 26959.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.048753 restraints weight = 21228.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.8188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7482  Z= 0.182
  Angle     :  0.712   8.648  10196  Z= 0.340
  Chirality :  0.041   0.150   1158
  Planarity :  0.005   0.043   1342
  Dihedral  :  4.685  20.107   1058
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.10 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.36 (0.25), residues: 958
  helix: -1.61 (0.25), residues: 332
  sheet: -0.78 (0.38), residues: 176
  loop : -1.77 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 426 
 HIS   0.006   0.001   HIS B 245 
 PHE   0.011   0.001   PHE A 389 
 TYR   0.010   0.002   TYR B 248 
 ARG   0.005   0.000   ARG A 126 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1844.98 seconds
wall clock time: 32 minutes 57.55 seconds (1977.55 seconds total)