Starting phenix.real_space_refine
on Fri Jan 17 17:53:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.cif"
  }
  resolution = 2.3
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1075 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      17      5.49       5
     S      63      5.16       5
     C    6585      2.51       5
     N    1804      2.21       5
     O    1998      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10467
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 591, 4771
          Classifications: {'peptide': 591}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 561}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 4702
          Classifications: {'peptide': 590}
          Link IDs: {'PTRANS': 31, 'TRANS': 558}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 608
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 6, 'TRANS': 68}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 283
          Classifications: {'RNA': 13}
          Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 8, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 3, 'rna3p': 9}
    Chain: "E"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 103
          Classifications: {'RNA': 5}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 2, 'rna3p': 2}
  Time building chain proxies: 6.52, per 1000 atoms: 0.62
  Number of scatterers: 10467
  At special positions: 0
  Unit cell: (92.402, 100.708, 126.663, 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      63     16.00
     P      17     15.00
     O    1998      8.00
     N    1804      7.00
     C    6585      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2386

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 12 sheets defined
      49.6% alpha, 11.6% beta
      2 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 3.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 16
    Processing helix  chain 'A' and resid 27 through 46
    Processing helix  chain 'A' and resid 103 through 107
    Processing helix  chain 'A' and resid 126 through 133
      removed outlier: 3.752A  pdb=" N   LEU A 131 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 155
      removed outlier: 4.745A  pdb=" N   GLY A 143 " --> pdb=" O   GLN A 139 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   PHE A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   CYS A 146 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 166
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 246 through 257
      removed outlier: 3.965A  pdb=" N   GLN A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 273 through 286
      removed outlier: 3.526A  pdb=" N   LEU A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 302
    Processing helix  chain 'A' and resid 304 through 316
    Processing helix  chain 'A' and resid 335 through 345
      removed outlier: 3.999A  pdb=" N   GLU A 339 " --> pdb=" O   PRO A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 4.433A  pdb=" N   ARG A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 401
      removed outlier: 3.710A  pdb=" N   GLN A 401 " --> pdb=" O   ARG A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 492
    Processing helix  chain 'A' and resid 493 through 497
    Processing helix  chain 'A' and resid 498 through 517
    Processing helix  chain 'A' and resid 540 through 557
    Processing helix  chain 'A' and resid 559 through 581
      removed outlier: 4.810A  pdb=" N   ARG A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LEU A 572 " --> pdb=" O   ASN A 568 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLU A 581 " --> pdb=" O   HIS A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 599
      removed outlier: 4.014A  pdb=" N   LYS A 596 " --> pdb=" O   ARG A 592 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL A 597 " --> pdb=" O   PRO A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 617
    Processing helix  chain 'B' and resid 1 through 5
    Processing helix  chain 'B' and resid 13 through 20
      removed outlier: 4.244A  pdb=" N   GLU B  17 " --> pdb=" O   THR B  14 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   TYR B  20 " --> pdb=" O   GLU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 47
      Proline residue:  B  44  - end of helix
    Processing helix  chain 'B' and resid 53 through 58
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 80 through 94
    Processing helix  chain 'B' and resid 95 through 108
      removed outlier: 3.622A  pdb=" N   LYS B 101 " --> pdb=" O   PRO B  97 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 113
      removed outlier: 3.713A  pdb=" N   LYS B 112 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 121
      removed outlier: 3.652A  pdb=" N   GLU B 117 " --> pdb=" O   LYS B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 151
    Processing helix  chain 'B' and resid 157 through 169
      removed outlier: 3.543A  pdb=" N   MET B 169 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 247 through 266
      removed outlier: 4.127A  pdb=" N   GLY B 252 " --> pdb=" O   MET B 248 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   PHE B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B 256 " --> pdb=" O   GLY B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 287
    Processing helix  chain 'B' and resid 310 through 326
      removed outlier: 3.728A  pdb=" N   MET B 314 " --> pdb=" O   ASP B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 344
      Proline residue:  B 338  - end of helix
      removed outlier: 3.557A  pdb=" N   SER B 344 " --> pdb=" O   MET B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 378
      removed outlier: 4.429A  pdb=" N   ARG B 378 " --> pdb=" O   ASP B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 409
      removed outlier: 3.618A  pdb=" N   SER B 400 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE B 408 " --> pdb=" O   ALA B 404 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLU B 409 " --> pdb=" O   LEU B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 449
      removed outlier: 3.552A  pdb=" N   LYS B 448 " --> pdb=" O   ARG B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 459
      removed outlier: 3.774A  pdb=" N   CYS B 459 " --> pdb=" O   PRO B 456 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 456 through 459'
    Processing helix  chain 'B' and resid 496 through 514
    Processing helix  chain 'B' and resid 518 through 537
      removed outlier: 3.674A  pdb=" N   TYR B 537 " --> pdb=" O   TYR B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 552
      removed outlier: 3.594A  pdb=" N   MET B 549 " --> pdb=" O   ARG B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 562
    Processing helix  chain 'B' and resid 575 through 583
    Processing helix  chain 'B' and resid 587 through 595
    Processing helix  chain 'C' and resid 52 through 55
    Processing helix  chain 'C' and resid 56 through 62
    Processing helix  chain 'C' and resid 102 through 111
      removed outlier: 3.921A  pdb=" N   LYS C 109 " --> pdb=" O   ASP C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 123
    Processing helix  chain 'C' and resid 124 through 136
      removed outlier: 3.688A  pdb=" N   LYS C 129 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL C 130 " --> pdb=" O   GLU C 126 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR C 136 " --> pdb=" O   ARG C 132 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88
      removed outlier: 3.782A  pdb=" N   LEU A 117 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211
    Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211
      removed outlier: 4.503A  pdb=" N   ASN B 453 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 238
      removed outlier: 4.253A  pdb=" N   ILE A 450 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   TRP A 426 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 423 through 431
    current: chain 'A' and resid 463 through 469
      removed outlier: 6.757A  pdb=" N   VAL A 464 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242
      removed outlier: 7.141A  pdb=" N   TRP A 426 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 442 through 451
    current: chain 'A' and resid 290 through 291
    Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323
    Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531
    Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 125
    Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175
    Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245
      removed outlier: 4.587A  pdb=" N   THR B 228 " --> pdb=" O   ASP B 348 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 469
    Processing sheet with id=AB3, first strand: chain 'B' and resid 633 through 634
      removed outlier: 4.697A  pdb=" N   THR B 633 " --> pdb=" O   SER C  68 " (cutoff:3.500A)

    463 hydrogen bonds defined for protein.
    1278 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      5 hydrogen bonds
      10 hydrogen bond angles
      0 basepair planarities
      2 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 3.34

  Time building geometry restraints manager: 2.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2846
        1.33 -     1.45: 1854
        1.45 -     1.57: 5896
        1.57 -     1.69: 33
        1.69 -     1.81: 105
  Bond restraints: 10734
  Sorted by residual:
  bond pdb=" CA  LYS A 170 "
       pdb=" CB  LYS A 170 "
    ideal  model  delta    sigma   weight residual
    1.518  1.541 -0.023 2.08e-02 2.31e+03 1.27e+00
  bond pdb=" C   ALA A 169 "
       pdb=" N   LYS A 170 "
    ideal  model  delta    sigma   weight residual
    1.325  1.338 -0.013 1.14e-02 7.69e+03 1.25e+00
  bond pdb=" CA  VAL B 491 "
       pdb=" CB  VAL B 491 "
    ideal  model  delta    sigma   weight residual
    1.546  1.538  0.009 8.80e-03 1.29e+04 9.61e-01
  bond pdb=" CA  ILE A 414 "
       pdb=" CB  ILE A 414 "
    ideal  model  delta    sigma   weight residual
    1.540  1.528  0.012 1.36e-02 5.41e+03 8.37e-01
  bond pdb=" CB  MET B 526 "
       pdb=" CG  MET B 526 "
    ideal  model  delta    sigma   weight residual
    1.520  1.498  0.022 3.00e-02 1.11e+03 5.58e-01
  ... (remaining 10729 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 14303
        1.38 -     2.76: 245
        2.76 -     4.14: 59
        4.14 -     5.51: 13
        5.51 -     6.89: 3
  Bond angle restraints: 14623
  Sorted by residual:
  angle pdb=" N   GLY B 352 "
        pdb=" CA  GLY B 352 "
        pdb=" C   GLY B 352 "
      ideal   model   delta    sigma   weight residual
     112.04  116.98   -4.94 1.02e+00 9.61e-01 2.35e+01
  angle pdb=" C   LYS A 170 "
        pdb=" CA  LYS A 170 "
        pdb=" CB  LYS A 170 "
      ideal   model   delta    sigma   weight residual
     115.79  111.83    3.96 1.19e+00 7.06e-01 1.11e+01
  angle pdb=" C   SER B   8 "
        pdb=" N   GLU B   9 "
        pdb=" CA  GLU B   9 "
      ideal   model   delta    sigma   weight residual
     121.54  126.53   -4.99 1.91e+00 2.74e-01 6.82e+00
  angle pdb=" C   TYR B 210 "
        pdb=" N   THR B 211 "
        pdb=" CA  THR B 211 "
      ideal   model   delta    sigma   weight residual
     121.54  126.05   -4.51 1.91e+00 2.74e-01 5.58e+00
  angle pdb=" CB  MET A 546 "
        pdb=" CG  MET A 546 "
        pdb=" SD  MET A 546 "
      ideal   model   delta    sigma   weight residual
     112.70  105.81    6.89 3.00e+00 1.11e-01 5.28e+00
  ... (remaining 14618 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 5978
       17.19 -    34.38: 428
       34.38 -    51.58: 80
       51.58 -    68.77: 29
       68.77 -    85.96: 15
  Dihedral angle restraints: 6530
    sinusoidal: 2854
      harmonic: 3676
  Sorted by residual:
  dihedral pdb=" CA  MET A 546 "
           pdb=" C   MET A 546 "
           pdb=" N   ILE A 547 "
           pdb=" CA  ILE A 547 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.37   23.63     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  ILE B 212 "
           pdb=" C   ILE B 212 "
           pdb=" N   LYS B 213 "
           pdb=" CA  LYS B 213 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.49  -17.51     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CG  ARG A 570 "
           pdb=" CD  ARG A 570 "
           pdb=" NE  ARG A 570 "
           pdb=" CZ  ARG A 570 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.09   44.91     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 6527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1025
       0.027 -    0.055: 390
       0.055 -    0.082: 132
       0.082 -    0.109: 73
       0.109 -    0.136: 25
  Chirality restraints: 1645
  Sorted by residual:
  chirality pdb=" CA  ILE B 460 "
            pdb=" N   ILE B 460 "
            pdb=" C   ILE B 460 "
            pdb=" CB  ILE B 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  ILE A 480 "
            pdb=" N   ILE A 480 "
            pdb=" C   ILE A 480 "
            pdb=" CB  ILE A 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE C  75 "
            pdb=" N   ILE C  75 "
            pdb=" C   ILE C  75 "
            pdb=" CB  ILE C  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  ... (remaining 1642 not shown)

  Planarity restraints: 1804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 555 "   -0.029 5.00e-02 4.00e+02   4.37e-02 3.05e+00
        pdb=" N   PRO B 556 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 556 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 556 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 418 "   -0.028 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO A 419 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 419 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 419 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 108 "    0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO A 109 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 109 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 109 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1801 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1798
        2.77 -     3.30: 10157
        3.30 -     3.83: 18189
        3.83 -     4.37: 22434
        4.37 -     4.90: 36834
  Nonbonded interactions: 89412
  Sorted by model distance:
  nonbonded pdb=" O   SER A 482 "
            pdb=" O2'   A D   3 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OE2 GLU A 122 "
            pdb=" NZ  LYS B 109 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" NH2 ARG A 264 "
            pdb=" O   TYR A 459 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" OD2 ASP B 362 "
            pdb=" NZ  LYS B 364 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OD1 ASN B  11 "
            pdb=" OG1 THR B  14 "
     model   vdw
     2.298 3.040
  ... (remaining 89407 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: 0.00
========== 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 individual isotropic
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:             0.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     28.380
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  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:12.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
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   0.029  10734  Z= 0.136
  Angle     :  0.484   6.893  14623  Z= 0.249
  Chirality :  0.038   0.136   1645
  Planarity :  0.004   0.044   1804
  Dihedral  : 13.262  85.961   4144
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  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:  0.02 (0.23), residues: 1240
  helix:  0.58 (0.22), residues: 543
  sheet:  0.43 (0.46), residues: 123
  loop : -0.55 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  65 
 HIS   0.006   0.001   HIS B 476 
 PHE   0.017   0.001   PHE A 483 
 TYR   0.015   0.001   TYR B  22 
 ARG   0.008   0.000   ARG B 131 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7519 (m110) cc_final: 0.7080 (m110)
REVERT: B  422 ASP cc_start: 0.7675 (p0) cc_final: 0.7249 (p0)
REVERT: B  575 ASP cc_start: 0.8128 (t70) cc_final: 0.7884 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 1.6655
  time to fit residues: 282.9072
Evaluate side-chains
  130 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0670
   chunk 64 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 98 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 114 optimal weight:    0.4980
   overall best weight:    1.4322

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 311 GLN
A 516 ASN
** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
B 132 ASN
B 148 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.122058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.082927 restraints weight = 13926.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.09
r_work: 0.2844 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  10734  Z= 0.230
  Angle     :  0.581   7.408  14623  Z= 0.299
  Chirality :  0.043   0.182   1645
  Planarity :  0.005   0.049   1804
  Dihedral  : 10.234  73.017   1629
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  7.23 %
    Favored  : 91.17 %
  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:  0.51 (0.24), residues: 1240
  helix:  1.21 (0.22), residues: 559
  sheet: -0.02 (0.45), residues: 128
  loop : -0.40 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 426 
 HIS   0.005   0.001   HIS A 577 
 PHE   0.018   0.002   PHE A 483 
 TYR   0.018   0.002   TYR A 489 
 ARG   0.013   0.001   ARG A 536 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.8737 (m110) cc_final: 0.8520 (m110)
REVERT: B   93 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7887 (mpp80)
REVERT: B  332 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8002 (mmm)
REVERT: C   68 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8490 (p)
  outliers start: 18
  outliers final: 5
  residues processed: 138
  average time/residue: 1.6615
  time to fit residues: 243.6433
Evaluate side-chains
  138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 ARG
Chi-restraints excluded: chain B residue   93 ARG
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  102 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 25 optimal weight:    0.0470
   chunk 59 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 2 optimal weight:   40.0000
   chunk 34 optimal weight:    3.9990
   chunk 89 optimal weight:    0.2980
   chunk 113 optimal weight:    5.9990
   overall best weight:    1.2684

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 311 GLN
A 358 ASN
A 516 ASN
B 148 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 131 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.120505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.081664 restraints weight = 14128.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 2.09
r_work: 0.2847 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10734  Z= 0.193
  Angle     :  0.525   7.808  14623  Z= 0.270
  Chirality :  0.041   0.164   1645
  Planarity :  0.004   0.038   1804
  Dihedral  : 10.214  73.146   1629
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  8.74 %
    Favored  : 89.21 %
  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:  0.71 (0.24), residues: 1240
  helix:  1.51 (0.22), residues: 560
  sheet: -0.24 (0.43), residues: 130
  loop : -0.38 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.005   0.001   HIS B 476 
 PHE   0.015   0.001   PHE A 483 
 TYR   0.014   0.001   TYR B 533 
 ARG   0.006   0.000   ARG B 151 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8439 (mmmm)
REVERT: A  489 TYR cc_start: 0.9034 (t80) cc_final: 0.8833 (t80)
REVERT: A  546 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8634 (ptm)
REVERT: B   17 GLU cc_start: 0.8549 (pt0) cc_final: 0.8207 (pt0)
REVERT: B  131 ARG cc_start: 0.8555 (ptt90) cc_final: 0.8298 (ptt90)
REVERT: B  383 ASN cc_start: 0.8736 (t0) cc_final: 0.8302 (t0)
REVERT: B  436 MET cc_start: 0.9156 (ttp) cc_final: 0.8870 (ttp)
REVERT: B  588 GLU cc_start: 0.7772 (tp30) cc_final: 0.7490 (tp30)
  outliers start: 23
  outliers final: 11
  residues processed: 143
  average time/residue: 1.5983
  time to fit residues: 242.7567
Evaluate side-chains
  140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  438 ARG
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  515 GLU
Chi-restraints excluded: chain A residue  546 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  108 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 112 optimal weight:    9.9990
   chunk 117 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.119274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.080015 restraints weight = 13908.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.07
r_work: 0.2817 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10734  Z= 0.220
  Angle     :  0.530   7.773  14623  Z= 0.273
  Chirality :  0.042   0.176   1645
  Planarity :  0.004   0.038   1804
  Dihedral  : 10.240  73.101   1629
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  :  8.92 %
    Favored  : 88.40 %
  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:  0.71 (0.24), residues: 1240
  helix:  1.57 (0.22), residues: 560
  sheet: -0.39 (0.43), residues: 130
  loop : -0.41 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 426 
 HIS   0.004   0.001   HIS B 476 
 PHE   0.013   0.001   PHE A 483 
 TYR   0.016   0.001   TYR B 533 
 ARG   0.008   0.000   ARG A 536 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8438 (mmmm)
REVERT: A  516 ASN cc_start: 0.8780 (m-40) cc_final: 0.8210 (m110)
REVERT: A  546 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8672 (ptm)
REVERT: B   17 GLU cc_start: 0.8612 (pt0) cc_final: 0.8292 (pt0)
REVERT: B  131 ARG cc_start: 0.8510 (ptt90) cc_final: 0.8248 (ptt90)
REVERT: B  383 ASN cc_start: 0.8855 (t0) cc_final: 0.8386 (t0)
  outliers start: 30
  outliers final: 12
  residues processed: 145
  average time/residue: 1.6053
  time to fit residues: 247.6644
Evaluate side-chains
  142 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  438 ARG
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  546 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  108 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 108 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 7 optimal weight:   40.0000
   chunk 105 optimal weight:    0.8980
   chunk 117 optimal weight:    0.0970
   chunk 25 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 109 optimal weight:    0.8980
   chunk 122 optimal weight:    4.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
B 148 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.081588 restraints weight = 13891.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.07
r_work: 0.2852 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10734  Z= 0.166
  Angle     :  0.505   7.025  14623  Z= 0.259
  Chirality :  0.040   0.166   1645
  Planarity :  0.004   0.042   1804
  Dihedral  : 10.181  73.190   1629
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  :  9.81 %
    Favored  : 87.87 %
  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 (0.24), residues: 1240
  helix:  1.70 (0.22), residues: 561
  sheet: -0.44 (0.43), residues: 130
  loop : -0.39 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 476 
 PHE   0.012   0.001   PHE B 214 
 TYR   0.019   0.001   TYR A 489 
 ARG   0.010   0.000   ARG A 536 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8447 (mmmm)
REVERT: A  489 TYR cc_start: 0.9063 (t80) cc_final: 0.8851 (t80)
REVERT: A  546 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8604 (ptm)
REVERT: B   17 GLU cc_start: 0.8573 (pt0) cc_final: 0.8279 (pt0)
REVERT: B  131 ARG cc_start: 0.8449 (ptt90) cc_final: 0.8217 (ptt90)
REVERT: B  383 ASN cc_start: 0.8914 (t0) cc_final: 0.8430 (t0)
REVERT: B  588 GLU cc_start: 0.7640 (tp30) cc_final: 0.7315 (tp30)
  outliers start: 26
  outliers final: 9
  residues processed: 144
  average time/residue: 1.6435
  time to fit residues: 251.3408
Evaluate side-chains
  140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 ARG
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  546 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   74 GLU
Chi-restraints excluded: chain C residue  102 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 125 optimal weight:    7.9990
   chunk 105 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 GLN
B 567 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.120484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.081147 restraints weight = 13866.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.06
r_work: 0.2814 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2689 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10734  Z= 0.177
  Angle     :  0.505   7.215  14623  Z= 0.258
  Chirality :  0.040   0.167   1645
  Planarity :  0.004   0.042   1804
  Dihedral  : 10.166  73.184   1629
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 10.79 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.24), residues: 1240
  helix:  1.75 (0.22), residues: 561
  sheet: -0.48 (0.43), residues: 130
  loop : -0.39 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.003   0.001   HIS B 476 
 PHE   0.011   0.001   PHE B 214 
 TYR   0.017   0.001   TYR A 489 
 ARG   0.012   0.000   ARG A 536 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8414 (mmmm)
REVERT: A  546 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8631 (ptm)
REVERT: B   17 GLU cc_start: 0.8588 (pt0) cc_final: 0.8276 (pt0)
REVERT: B  131 ARG cc_start: 0.8427 (ptt90) cc_final: 0.8122 (ptt90)
REVERT: B  151 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7580 (mmm160)
REVERT: B  332 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8281 (mtm)
REVERT: B  383 ASN cc_start: 0.8917 (t0) cc_final: 0.8377 (t0)
REVERT: B  588 GLU cc_start: 0.7770 (tp30) cc_final: 0.7471 (tp30)
  outliers start: 22
  outliers final: 12
  residues processed: 138
  average time/residue: 1.7107
  time to fit residues: 250.9011
Evaluate side-chains
  138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  438 ARG
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  546 MET
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   74 GLU
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  108 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 91 optimal weight:    9.9990
   chunk 108 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 GLN
B 475 HIS
C 131 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.120722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.081455 restraints weight = 13974.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 2.06
r_work: 0.2853 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10734  Z= 0.164
  Angle     :  0.499   6.993  14623  Z= 0.255
  Chirality :  0.040   0.164   1645
  Planarity :  0.004   0.051   1804
  Dihedral  : 10.139  73.200   1629
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.70 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.24), residues: 1240
  helix:  1.86 (0.22), residues: 553
  sheet: -0.50 (0.43), residues: 130
  loop : -0.39 (0.25), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.003   0.001   HIS B 476 
 PHE   0.011   0.001   PHE B 214 
 TYR   0.016   0.001   TYR B 533 
 ARG   0.014   0.000   ARG A 536 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8448 (mmmm)
REVERT: A  546 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8617 (ptm)
REVERT: B   17 GLU cc_start: 0.8598 (pt0) cc_final: 0.8295 (pt0)
REVERT: B  131 ARG cc_start: 0.8441 (ptt90) cc_final: 0.8158 (ptt90)
REVERT: B  151 ARG cc_start: 0.7836 (mmm160) cc_final: 0.7615 (mmm160)
REVERT: B  383 ASN cc_start: 0.8885 (t0) cc_final: 0.8342 (t0)
REVERT: B  588 GLU cc_start: 0.7810 (tp30) cc_final: 0.7447 (tp30)
REVERT: C   72 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8741 (p)
  outliers start: 23
  outliers final: 9
  residues processed: 138
  average time/residue: 1.6277
  time to fit residues: 238.7613
Evaluate side-chains
  136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 ARG
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  546 MET
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  108 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0470
   chunk 95 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 113 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    2.4086

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

Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
A 577 HIS
B 148 GLN
B 475 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.117721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.078110 restraints weight = 13780.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.05
r_work: 0.2757 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2630 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10734  Z= 0.298
  Angle     :  0.571   8.370  14623  Z= 0.293
  Chirality :  0.043   0.190   1645
  Planarity :  0.005   0.055   1804
  Dihedral  : 10.283  73.015   1629
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 10.70 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.23), residues: 1240
  helix:  1.54 (0.22), residues: 567
  sheet: -0.54 (0.43), residues: 130
  loop : -0.55 (0.25), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 426 
 HIS   0.004   0.001   HIS B 531 
 PHE   0.013   0.002   PHE B  48 
 TYR   0.018   0.002   TYR A 489 
 ARG   0.013   0.001   ARG A 536 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8402 (mmmm)
REVERT: A  472 LYS cc_start: 0.8512 (mtmp) cc_final: 0.8128 (mtpp)
REVERT: B   17 GLU cc_start: 0.8607 (pt0) cc_final: 0.8307 (pt0)
REVERT: B   93 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8042 (mtp85)
REVERT: B  131 ARG cc_start: 0.8417 (ptt90) cc_final: 0.8167 (ptt90)
REVERT: B  151 ARG cc_start: 0.7852 (mmm160) cc_final: 0.7585 (mmm160)
REVERT: B  383 ASN cc_start: 0.9019 (t0) cc_final: 0.8734 (t0)
REVERT: C   98 ARG cc_start: 0.8483 (ptm-80) cc_final: 0.8038 (mtm-85)
  outliers start: 25
  outliers final: 11
  residues processed: 139
  average time/residue: 1.6352
  time to fit residues: 241.3184
Evaluate side-chains
  134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  438 ARG
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   93 ARG
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  108 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 112 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9980
   chunk 113 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 110 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
B 148 GLN
B 475 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.120264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.080900 restraints weight = 14004.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.08
r_work: 0.2843 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  10734  Z= 0.161
  Angle     :  0.510   5.604  14623  Z= 0.261
  Chirality :  0.040   0.158   1645
  Planarity :  0.004   0.056   1804
  Dihedral  : 10.152  73.265   1629
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.69 %
    Favored  : 86.80 %
  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:  0.85 (0.24), residues: 1240
  helix:  1.83 (0.22), residues: 553
  sheet: -0.55 (0.43), residues: 130
  loop : -0.40 (0.25), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 330 
 HIS   0.003   0.001   HIS A 577 
 PHE   0.011   0.001   PHE B 214 
 TYR   0.017   0.001   TYR B 533 
 ARG   0.014   0.000   ARG A 536 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 1.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8470 (mmmm)
REVERT: B   17 GLU cc_start: 0.8598 (pt0) cc_final: 0.8299 (pt0)
REVERT: B  131 ARG cc_start: 0.8407 (ptt90) cc_final: 0.8203 (ptt90)
REVERT: B  151 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7593 (mmm160)
REVERT: B  383 ASN cc_start: 0.8934 (t0) cc_final: 0.8631 (t0)
REVERT: B  588 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7178 (tp30)
REVERT: C   72 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8758 (p)
REVERT: C   98 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8115 (mtm-85)
  outliers start: 17
  outliers final: 8
  residues processed: 134
  average time/residue: 1.6576
  time to fit residues: 236.4499
Evaluate side-chains
  133 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 ARG
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  108 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:   20.0000
   chunk 29 optimal weight:    1.9990
   chunk 120 optimal weight:    0.3980
   chunk 66 optimal weight:   10.0000
   chunk 78 optimal weight:    0.0270
   chunk 110 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    1.0042

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

Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
B 148 GLN
B 475 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.120214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.080920 restraints weight = 13917.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.06
r_work: 0.2844 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10734  Z= 0.170
  Angle     :  0.511   6.304  14623  Z= 0.260
  Chirality :  0.040   0.152   1645
  Planarity :  0.004   0.060   1804
  Dihedral  : 10.122  73.178   1629
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.95 %
    Favored  : 86.89 %
  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:  0.90 (0.24), residues: 1240
  helix:  1.86 (0.22), residues: 553
  sheet: -0.54 (0.43), residues: 130
  loop : -0.36 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.003   0.001   HIS B 476 
 PHE   0.011   0.001   PHE B 214 
 TYR   0.016   0.001   TYR B 533 
 ARG   0.015   0.000   ARG A 536 

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8468 (mmmm)
REVERT: B   17 GLU cc_start: 0.8579 (pt0) cc_final: 0.8274 (pt0)
REVERT: B   93 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7942 (mtp85)
REVERT: B  131 ARG cc_start: 0.8413 (ptt90) cc_final: 0.8140 (ptt90)
REVERT: B  151 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7583 (mmm160)
REVERT: B  383 ASN cc_start: 0.8953 (t0) cc_final: 0.8656 (t0)
REVERT: C   72 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8810 (p)
REVERT: C   98 ARG cc_start: 0.8469 (ptm-80) cc_final: 0.8099 (mtm-85)
  outliers start: 13
  outliers final: 6
  residues processed: 129
  average time/residue: 1.6633
  time to fit residues: 228.0369
Evaluate side-chains
  129 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 ARG
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   93 ARG
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  102 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 118 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 3 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
B 148 GLN
B 475 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.117708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.078110 restraints weight = 13726.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.04
r_work: 0.2759 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2632 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10734  Z= 0.306
  Angle     :  0.571   7.236  14623  Z= 0.293
  Chirality :  0.043   0.169   1645
  Planarity :  0.005   0.064   1804
  Dihedral  : 10.246  73.050   1629
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.69 %
    Favored  : 86.80 %
  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:  0.61 (0.24), residues: 1240
  helix:  1.56 (0.22), residues: 567
  sheet: -0.58 (0.44), residues: 133
  loop : -0.52 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 426 
 HIS   0.006   0.001   HIS A 577 
 PHE   0.013   0.002   PHE B  48 
 TYR   0.018   0.002   TYR A 489 
 ARG   0.015   0.000   ARG A 536 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10247.22 seconds
wall clock time: 183 minutes 27.47 seconds (11007.47 seconds total)