Starting phenix.real_space_refine
on Fri Dec  8 07:41:47 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/12_2023/7r9o_24330.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/12_2023/7r9o_24330.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/12_2023/7r9o_24330.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/12_2023/7r9o_24330.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/12_2023/7r9o_24330.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/12_2023/7r9o_24330.pdb"
  }
  resolution = 4.0
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    2351      2.51       5
     N     655      2.21       5
     O     759      1.98       5
     H    3938      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "J ARG  382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "J PHE  433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J ARG  522": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7726
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "J"
      Number of atoms: 7726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 7726
          Classifications: {'peptide': 505}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 496}
  Time building chain proxies: 4.00, per 1000 atoms: 0.52
  Number of scatterers: 7726
  At special positions: 0
  Unit cell: (82.08, 70.2, 111.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     O     759      8.00
     N     655      7.00
     C    2351      6.00
     H    3938      1.00
    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  - 3.50
        Amino acid           : False - 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: 5.78
  Conformation dependent library (CDL) restraints added in 893.3 milliseconds
  

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  938

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 4 sheets defined
      52.3% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'J' and resid 20 through 34
      removed outlier: 3.628A  pdb=" N   ASN J  24 " --> pdb=" O   ALA J  20 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU J  26 " --> pdb=" O   ARG J  22 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ARG J  29 " --> pdb=" O   ILE J  25 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 61 through 66
    Processing helix  chain 'J' and resid 72 through 74
      No H-bonds generated for 'chain 'J' and resid 72 through 74'
    Processing helix  chain 'J' and resid 75 through 87
      removed outlier: 3.779A  pdb=" N   ILE J  79 " --> pdb=" O   ALA J  75 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL J  81 " --> pdb=" O   MET J  77 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA J  82 " --> pdb=" O   LEU J  78 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR J  84 " --> pdb=" O   GLU J  80 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN J  85 " --> pdb=" O   VAL J  81 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LYS J  87 " --> pdb=" O   LYS J  83 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 92 through 112
      removed outlier: 3.502A  pdb=" N   VAL J  98 " --> pdb=" O   THR J  94 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL J  99 " --> pdb=" O   THR J  95 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ALA J 100 " --> pdb=" O   ALA J  96 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU J 102 " --> pdb=" O   VAL J  98 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA J 107 " --> pdb=" O   LEU J 103 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLU J 108 " --> pdb=" O   LEU J 104 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   GLU J 109 " --> pdb=" O   ARG J 105 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU J 110 " --> pdb=" O   LYS J 106 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 139
      removed outlier: 3.848A  pdb=" N   VAL J 120 " --> pdb=" O   HIS J 116 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LYS J 122 " --> pdb=" O   THR J 118 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLY J 123 " --> pdb=" O   ILE J 119 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   TYR J 124 " --> pdb=" O   VAL J 120 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLN J 125 " --> pdb=" O   VAL J 121 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLN J 132 " --> pdb=" O   ALA J 128 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLU J 133 " --> pdb=" O   GLN J 129 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU J 134 " --> pdb=" O   LYS J 130 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   LYS J 136 " --> pdb=" O   GLN J 132 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   THR J 137 " --> pdb=" O   GLU J 133 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 146 through 162
      removed outlier: 3.729A  pdb=" N   LYS J 152 " --> pdb=" O   GLU J 148 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR J 156 " --> pdb=" O   LYS J 152 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY J 162 " --> pdb=" O   ILE J 158 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 167 through 180
      removed outlier: 3.608A  pdb=" N   ALA J 171 " --> pdb=" O   LYS J 167 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU J 172 " --> pdb=" O   GLU J 168 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 189 through 193
    Processing helix  chain 'J' and resid 257 through 279
      removed outlier: 3.671A  pdb=" N   PHE J 261 " --> pdb=" O   LYS J 257 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLU J 263 " --> pdb=" O   MET J 259 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU J 266 " --> pdb=" O   ILE J 262 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   MET J 272 " --> pdb=" O   MET J 268 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU J 275 " --> pdb=" O   ASP J 271 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE J 276 " --> pdb=" O   MET J 272 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 293 through 301
      removed outlier: 3.785A  pdb=" N   TYR J 297 " --> pdb=" O   LEU J 293 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 310 through 322
      removed outlier: 3.653A  pdb=" N   MET J 314 " --> pdb=" O   LYS J 310 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LYS J 316 " --> pdb=" O   SER J 312 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LEU J 317 " --> pdb=" O   ASP J 313 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ALA J 318 " --> pdb=" O   MET J 314 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS J 319 " --> pdb=" O   GLU J 315 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 373 through 383
      removed outlier: 3.723A  pdb=" N   GLU J 378 " --> pdb=" O   GLU J 374 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL J 380 " --> pdb=" O   VAL J 376 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 386 through 398
    Processing helix  chain 'J' and resid 405 through 420
      removed outlier: 3.592A  pdb=" N   VAL J 409 " --> pdb=" O   GLY J 405 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU J 410 " --> pdb=" O   SER J 406 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER J 412 " --> pdb=" O   GLU J 408 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   MET J 413 " --> pdb=" O   VAL J 409 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLU J 417 " --> pdb=" O   MET J 413 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 424 through 427
      removed outlier: 3.578A  pdb=" N   GLN J 427 " --> pdb=" O   GLY J 424 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 424 through 427'
    Processing helix  chain 'J' and resid 428 through 437
      removed outlier: 3.803A  pdb=" N   LEU J 437 " --> pdb=" O   PHE J 433 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 438 through 448
      removed outlier: 3.946A  pdb=" N   ARG J 442 " --> pdb=" O   GLU J 438 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA J 448 " --> pdb=" O   LEU J 444 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 455 through 463
      removed outlier: 3.823A  pdb=" N   ARG J 460 " --> pdb=" O   LEU J 456 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA J 461 " --> pdb=" O   VAL J 457 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA J 462 " --> pdb=" O   LYS J 458 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   HIS J 463 " --> pdb=" O   VAL J 459 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 482 through 487
    Processing helix  chain 'J' and resid 492 through 512
      removed outlier: 3.550A  pdb=" N   ALA J 503 " --> pdb=" O   ILE J 499 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU J 507 " --> pdb=" O   ALA J 503 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   MET J 508 " --> pdb=" O   GLU J 504 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   LEU J 509 " --> pdb=" O   SER J 505 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE J 512 " --> pdb=" O   MET J 508 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'J' and resid 140 through 141
      removed outlier: 3.716A  pdb=" N   ILE J 400 " --> pdb=" O   CYS J 140 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   VAL J 401 " --> pdb=" O   GLU J 490 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLU J 490 " --> pdb=" O   VAL J 401 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 196 through 197
      removed outlier: 3.560A  pdb=" N   THR J 366 " --> pdb=" O   ILE J 209 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE J 209 " --> pdb=" O   THR J 366 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 228 through 230
      removed outlier: 7.653A  pdb=" N   THR J 228 " --> pdb=" O   LEU J 342 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LEU J 342 " --> pdb=" O   THR J 228 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLU J 344 " --> pdb=" O   PHE J 355 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE J 355 " --> pdb=" O   GLU J 344 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 472 through 473

    126 hydrogen bonds defined for protein.
    360 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.12

  Time building geometry restraints manager: 6.05 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3931
        1.03 -     1.23: 7
        1.23 -     1.42: 1405
        1.42 -     1.61: 2365
        1.61 -     1.81: 39
  Bond restraints: 7747
  Sorted by residual:
  bond pdb=" CA  LEU J 368 "
       pdb=" CB  LEU J 368 "
    ideal  model  delta    sigma   weight residual
    1.530  1.541 -0.011 1.69e-02 3.50e+03 4.05e-01
  bond pdb=" N   LYS J 161 "
       pdb=" CA  LYS J 161 "
    ideal  model  delta    sigma   weight residual
    1.468  1.461  0.008 1.24e-02 6.50e+03 3.82e-01
  bond pdb=" CA  GLU J 358 "
       pdb=" C   GLU J 358 "
    ideal  model  delta    sigma   weight residual
    1.523  1.531 -0.008 1.34e-02 5.57e+03 3.59e-01
  bond pdb=" N   VAL J 384 "
       pdb=" CA  VAL J 384 "
    ideal  model  delta    sigma   weight residual
    1.452  1.459 -0.007 1.18e-02 7.18e+03 3.57e-01
  bond pdb=" CA  VAL J 439 "
       pdb=" C   VAL J 439 "
    ideal  model  delta    sigma   weight residual
    1.519  1.526 -0.007 1.14e-02 7.69e+03 3.45e-01
  ... (remaining 7742 not shown)

  Histogram of bond angle deviations from ideal:
      100.87 -   106.95: 59
      106.95 -   113.02: 9888
      113.02 -   119.10: 1576
      119.10 -   125.18: 2569
      125.18 -   131.26: 53
  Bond angle restraints: 14145
  Sorted by residual:
  angle pdb=" N   VAL J 384 "
        pdb=" CA  VAL J 384 "
        pdb=" C   VAL J 384 "
      ideal   model   delta    sigma   weight residual
     112.96  109.07    3.89 1.00e+00 1.00e+00 1.52e+01
  angle pdb=" N   THR J 253 "
        pdb=" CA  THR J 253 "
        pdb=" C   THR J 253 "
      ideal   model   delta    sigma   weight residual
     114.62  111.25    3.37 1.14e+00 7.69e-01 8.74e+00
  angle pdb=" CA  THR J 253 "
        pdb=" C   THR J 253 "
        pdb=" N   ASP J 254 "
      ideal   model   delta    sigma   weight residual
     119.71  117.13    2.58 1.17e+00 7.31e-01 4.86e+00
  angle pdb=" CA  VAL J 384 "
        pdb=" C   VAL J 384 "
        pdb=" N   ASP J 385 "
      ideal   model   delta    sigma   weight residual
     118.65  116.71    1.94 1.07e+00 8.73e-01 3.30e+00
  angle pdb=" CA  VAL J 384 "
        pdb=" C   VAL J 384 "
        pdb=" O   VAL J 384 "
      ideal   model   delta    sigma   weight residual
     119.29  120.73   -1.44 8.40e-01 1.42e+00 2.93e+00
  ... (remaining 14140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.03: 3311
       13.03 -    26.06: 69
       26.06 -    39.09: 24
       39.09 -    52.12: 4
       52.12 -    65.15: 3
  Dihedral angle restraints: 3411
    sinusoidal: 1911
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" CA  ARG J  18 "
           pdb=" CB  ARG J  18 "
           pdb=" CG  ARG J  18 "
           pdb=" CD  ARG J  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -93.31   33.31     3      1.50e+01 4.44e-03 5.56e+00
  dihedral pdb=" CB  MET J  77 "
           pdb=" CG  MET J  77 "
           pdb=" SD  MET J  77 "
           pdb=" CE  MET J  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   89.03  -29.03     3      1.50e+01 4.44e-03 4.50e+00
  dihedral pdb=" CA  VAL J 401 "
           pdb=" CB  VAL J 401 "
           pdb=" CG1 VAL J 401 "
           pdb="HG13 VAL J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -120.00  -54.85  -65.15     2      3.00e+01 1.11e-03 4.39e+00
  ... (remaining 3408 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 397
       0.025 -    0.051: 140
       0.051 -    0.076: 44
       0.076 -    0.102: 30
       0.102 -    0.127: 19
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  ILE J 303 "
            pdb=" N   ILE J 303 "
            pdb=" C   ILE J 303 "
            pdb=" CB  ILE J 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE J 195 "
            pdb=" N   ILE J 195 "
            pdb=" C   ILE J 195 "
            pdb=" CB  ILE J 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  ILE J 209 "
            pdb=" N   ILE J 209 "
            pdb=" C   ILE J 209 "
            pdb=" CB  ILE J 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.63e-01
  ... (remaining 627 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS J 116 "    0.008 5.00e-02 4.00e+02   1.22e-02 2.36e-01
        pdb=" N   PRO J 117 "   -0.021 5.00e-02 4.00e+02
        pdb=" CA  PRO J 117 "    0.006 5.00e-02 4.00e+02
        pdb=" CD  PRO J 117 "    0.007 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY J  40 "    0.007 5.00e-02 4.00e+02   1.05e-02 1.78e-01
        pdb=" N   PRO J  41 "   -0.018 5.00e-02 4.00e+02
        pdb=" CA  PRO J  41 "    0.005 5.00e-02 4.00e+02
        pdb=" CD  PRO J  41 "    0.006 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP J 254 "   -0.007 5.00e-02 4.00e+02   1.05e-02 1.78e-01
        pdb=" N   PRO J 255 "    0.018 5.00e-02 4.00e+02
        pdb=" CA  PRO J 255 "   -0.005 5.00e-02 4.00e+02
        pdb=" CD  PRO J 255 "   -0.006 5.00e-02 4.00e+02
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 846
        2.27 -     2.85: 18213
        2.85 -     3.43: 17566
        3.43 -     4.02: 22640
        4.02 -     4.60: 35430
  Nonbonded interactions: 94695
  Sorted by model distance:
  nonbonded pdb=" HZ1 LYS J 169 "
            pdb=" O   ASP J 204 "
     model   vdw
     1.687 1.850
  nonbonded pdb=" OE1 GLU J 408 "
            pdb=" H   GLU J 408 "
     model   vdw
     1.695 1.850
  nonbonded pdb=" O   LEU J 317 "
            pdb=" HG1 THR J 321 "
     model   vdw
     1.715 1.850
  nonbonded pdb=" OD1 ASN J 236 "
            pdb=" HZ1 LYS J 311 "
     model   vdw
     1.718 1.850
  nonbonded pdb=" O   ILE J  64 "
            pdb=" H   MET J  68 "
     model   vdw
     1.729 1.850
  ... (remaining 94690 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.920
  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:             0.130
  Extract box with map and model:          4.730
  Check model and map are aligned:         0.130
  Set scattering table:                    0.070
  Process input model:                     28.770
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
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      :  0.002   0.012   3809  Z= 0.107
  Angle     :  0.381   3.992   5126  Z= 0.231
  Chirality :  0.038   0.127    630
  Planarity :  0.001   0.012    663
  Dihedral  :  4.489  61.236   1463
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  : 10.54 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.72 %
    Favored  : 98.03 %
  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: -4.93 (0.27), residues: 503
  helix: -3.96 (0.20), residues: 212
  sheet: -4.24 (0.66), residues: 31
  loop : -2.47 (0.32), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS J  72 
   PHE   0.001   0.000   PHE J 285 
   TYR   0.001   0.000   TYR J 418 
   ARG   0.001   0.000   ARG J 308 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 69
  average time/residue: 0.5063
  time to fit residues: 40.4791
Evaluate side-chains
  44 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.503 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0782
  time to fit residues: 0.7600
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0670
   chunk 25 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7120

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

Flipped N/Q/H residues before XYZ refinement:
J 447 ASN
J 486 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3809  Z= 0.182
  Angle     :  0.528   4.591   5126  Z= 0.281
  Chirality :  0.039   0.128    630
  Planarity :  0.004   0.038    663
  Dihedral  :  2.744  10.765    529
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.62 %
    Favored  : 92.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.45 (0.32), residues: 503
  helix: -2.01 (0.29), residues: 230
  sheet: -4.00 (0.66), residues: 31
  loop : -2.26 (0.34), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS J 375 
   PHE   0.003   0.001   PHE J 285 
   TYR   0.009   0.002   TYR J 124 
   ARG   0.006   0.001   ARG J  66 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 40
  average time/residue: 0.2316
  time to fit residues: 13.2466
Evaluate side-chains
  30 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.591 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1188
  time to fit residues: 0.8972
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    0.3980
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.4948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3809  Z= 0.210
  Angle     :  0.519   4.519   5126  Z= 0.279
  Chirality :  0.038   0.131    630
  Planarity :  0.003   0.036    663
  Dihedral  :  2.978  11.462    529
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.11 %
    Favored  : 91.15 %
  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: -1.94 (0.35), residues: 503
  helix: -0.52 (0.33), residues: 224
  sheet: -3.40 (0.74), residues: 31
  loop : -1.69 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS J 116 
   PHE   0.009   0.001   PHE J 285 
   TYR   0.012   0.002   TYR J 124 
   ARG   0.003   0.000   ARG J  66 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 29
  average time/residue: 0.2223
  time to fit residues: 9.4177
Evaluate side-chains
  27 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.651 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 2
  average time/residue: 0.0923
  time to fit residues: 1.1331
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 23 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
J 474 ASN
J 500 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.6104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3809  Z= 0.256
  Angle     :  0.546   4.591   5126  Z= 0.295
  Chirality :  0.039   0.128    630
  Planarity :  0.003   0.032    663
  Dihedral  :  3.464  12.471    529
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.57 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.35), residues: 503
  helix: -0.22 (0.32), residues: 238
  sheet: -3.22 (0.88), residues: 31
  loop : -1.62 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS J 116 
   PHE   0.005   0.001   PHE J 285 
   TYR   0.013   0.002   TYR J 124 
   ARG   0.003   0.000   ARG J  66 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 28
  average time/residue: 0.2596
  time to fit residues: 10.2668
Evaluate side-chains
  24 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.538 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 2
  average time/residue: 0.0949
  time to fit residues: 0.9090
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.6396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3809  Z= 0.178
  Angle     :  0.473   4.907   5126  Z= 0.252
  Chirality :  0.038   0.130    630
  Planarity :  0.002   0.018    663
  Dihedral  :  3.287  12.092    529
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 11.79 %
    Favored  : 87.96 %
  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: -1.25 (0.36), residues: 503
  helix:  0.16 (0.32), residues: 241
  sheet: -3.10 (0.91), residues: 31
  loop : -1.53 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS J 116 
   PHE   0.006   0.001   PHE J 285 
   TYR   0.007   0.001   TYR J 124 
   ARG   0.001   0.000   ARG J 218 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 27
  average time/residue: 0.2865
  time to fit residues: 10.7628
Evaluate side-chains
  24 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.747 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.0985
  time to fit residues: 0.9776
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    0.4980
   chunk 16 optimal weight:    0.4980
   chunk 25 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0040
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.5592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.6525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3809  Z= 0.134
  Angle     :  0.457   4.533   5126  Z= 0.237
  Chirality :  0.038   0.128    630
  Planarity :  0.002   0.018    663
  Dihedral  :  3.173  11.686    529
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.79 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.37), residues: 503
  helix:  0.46 (0.33), residues: 241
  sheet: -2.93 (0.84), residues: 36
  loop : -1.36 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS J 463 
   PHE   0.011   0.001   PHE J 285 
   TYR   0.005   0.001   TYR J 124 
   ARG   0.002   0.000   ARG J 105 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 27
  average time/residue: 0.2815
  time to fit residues: 10.6231
Evaluate side-chains
  25 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.685 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.1003
  time to fit residues: 1.0380
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0050
   chunk 32 optimal weight:   10.0000
   overall best weight:    0.7394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.6720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3809  Z= 0.145
  Angle     :  0.453   4.806   5126  Z= 0.236
  Chirality :  0.038   0.128    630
  Planarity :  0.002   0.017    663
  Dihedral  :  3.172  12.438    529
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.30 %
    Favored  : 88.21 %
  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: -0.80 (0.36), residues: 503
  helix:  0.58 (0.33), residues: 242
  sheet: -2.89 (0.87), residues: 31
  loop : -1.38 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS J 116 
   PHE   0.009   0.001   PHE J 285 
   TYR   0.005   0.001   TYR J 124 
   ARG   0.001   0.000   ARG J 218 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 28
  average time/residue: 0.2738
  time to fit residues: 10.8203
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.756 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 2
  average time/residue: 0.0939
  time to fit residues: 1.2231
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0570
   chunk 46 optimal weight:    0.0010
   chunk 42 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.4104

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.6789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3809  Z= 0.125
  Angle     :  0.459   4.960   5126  Z= 0.234
  Chirality :  0.039   0.128    630
  Planarity :  0.002   0.017    663
  Dihedral  :  3.122  15.498    529
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 11.55 %
    Favored  : 88.21 %
  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: -0.62 (0.37), residues: 503
  helix:  0.73 (0.33), residues: 242
  sheet: -2.83 (0.86), residues: 31
  loop : -1.28 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS J 463 
   PHE   0.009   0.001   PHE J 285 
   TYR   0.003   0.001   TYR J 124 
   ARG   0.001   0.000   ARG J 218 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 27
  average time/residue: 0.2705
  time to fit residues: 10.1595
Evaluate side-chains
  25 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.603 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.1030
  time to fit residues: 1.0061
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.6998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3809  Z= 0.149
  Angle     :  0.473   5.535   5126  Z= 0.245
  Chirality :  0.039   0.137    630
  Planarity :  0.002   0.017    663
  Dihedral  :  3.148  15.357    529
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 12.53 %
    Favored  : 87.22 %
  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: -0.59 (0.37), residues: 503
  helix:  0.72 (0.33), residues: 242
  sheet: -2.78 (0.85), residues: 31
  loop : -1.23 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS J 116 
   PHE   0.008   0.001   PHE J 285 
   TYR   0.006   0.001   TYR J 124 
   ARG   0.001   0.000   ARG J 431 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 26
  average time/residue: 0.2809
  time to fit residues: 10.3029
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.726 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.1001
  time to fit residues: 1.0703
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 31 optimal weight:    0.2980
   chunk 42 optimal weight:    0.4980
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.7141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3809  Z= 0.130
  Angle     :  0.468   5.672   5126  Z= 0.239
  Chirality :  0.039   0.129    630
  Planarity :  0.002   0.017    663
  Dihedral  :  3.112  14.249    529
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 12.53 %
    Favored  : 87.22 %
  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: -0.54 (0.37), residues: 503
  helix:  0.78 (0.33), residues: 245
  sheet: -2.71 (0.83), residues: 31
  loop : -1.25 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS J 296 
   PHE   0.008   0.001   PHE J 285 
   TYR   0.004   0.001   TYR J 124 
   ARG   0.002   0.000   ARG J 218 

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 26
  average time/residue: 0.2844
  time to fit residues: 10.3204
Evaluate side-chains
  23 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.654 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.1066
  time to fit residues: 1.1264
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 7 optimal weight:    0.2980
   chunk 34 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** J 222 GLN ** 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 = 0.3705 r_free = 0.3705 target = 0.067732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.044512 restraints weight = 70454.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.046198 restraints weight = 32710.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.047281 restraints weight = 20005.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.7355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   3809  Z= 0.155
  Angle     :  0.518   9.789   5126  Z= 0.262
  Chirality :  0.039   0.130    630
  Planarity :  0.002   0.017    663
  Dihedral  :  3.187  16.500    529
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 13.02 %
    Favored  : 86.73 %
  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: -0.54 (0.37), residues: 503
  helix:  0.75 (0.33), residues: 245
  sheet: -2.74 (0.82), residues: 31
  loop : -1.20 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS J 116 
   PHE   0.008   0.001   PHE J 285 
   TYR   0.005   0.001   TYR J 124 
   ARG   0.001   0.000   ARG J 105 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2333.60 seconds
wall clock time: 45 minutes 9.34 seconds (2709.34 seconds total)