Starting phenix.real_space_refine
on Sun Jul 27 20:58:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7adj_11727/07_2025/7adj_11727.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7adj_11727/07_2025/7adj_11727.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7adj_11727/07_2025/7adj_11727.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7adj_11727/07_2025/7adj_11727.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7adj_11727/07_2025/7adj_11727.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7adj_11727/07_2025/7adj_11727.cif"
  }
  resolution = 2.8
  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=   1.000
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       3      5.16       5
     C    3078      2.51       5
     N     850      2.21       5
     O     989      1.98       5
     H    4790      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9710
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 613, 9710
          Classifications: {'peptide': 613}
          Link IDs: {'PTRANS': 22, 'TRANS': 590}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 5.25, per 1000 atoms: 0.54
  Number of scatterers: 9710
  At special positions: 0
  Unit cell: (97.94, 97.94, 102.92, 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       3     16.00
     O     989      8.00
     N     850      7.00
     C    3078      6.00
     H    4790      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  - 3.00
        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: 2.73
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1142

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      37.2% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 152 through 158
    Processing helix  chain 'A' and resid 181 through 195
    Processing helix  chain 'A' and resid 209 through 219
      removed outlier: 3.635A  pdb=" N   GLU A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 226 through 236
      removed outlier: 3.529A  pdb=" N   VAL A 234 " --> pdb=" O   SER A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 254
      removed outlier: 4.335A  pdb=" N   LYS A 251 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   MET A 252 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 268
      removed outlier: 3.932A  pdb=" N   LYS A 263 " --> pdb=" O   ASN A 260 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   SER A 264 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   GLU A 265 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN A 267 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 274
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 279 through 289
      removed outlier: 3.779A  pdb=" N   TRP A 286 " --> pdb=" O   GLN A 282 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 287 " --> pdb=" O   GLU A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 291
      No H-bonds generated for 'chain 'A' and resid 290 through 291'
    Processing helix  chain 'A' and resid 292 through 296
    Processing helix  chain 'A' and resid 300 through 309
      removed outlier: 3.796A  pdb=" N   LYS A 305 " --> pdb=" O   SER A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 337
    Processing helix  chain 'A' and resid 338 through 351
      removed outlier: 3.814A  pdb=" N   SER A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 370
    Processing helix  chain 'A' and resid 380 through 388
      removed outlier: 4.354A  pdb=" N   TYR A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 394
    Processing helix  chain 'A' and resid 425 through 443
      removed outlier: 3.523A  pdb=" N   TYR A 429 " --> pdb=" O   ASN A 425 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   LYS A 433 " --> pdb=" O   TYR A 429 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   GLU A 434 " --> pdb=" O   ARG A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 468
    Processing helix  chain 'A' and resid 518 through 523
    Processing helix  chain 'A' and resid 557 through 561
    Processing helix  chain 'A' and resid 566 through 578
      removed outlier: 3.821A  pdb=" N   VAL A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 588
      removed outlier: 3.610A  pdb=" N   GLY A 588 " --> pdb=" O   PHE A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 603
    Processing helix  chain 'A' and resid 655 through 659
      removed outlier: 3.747A  pdb=" N   GLU A 659 " --> pdb=" O   GLU A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 710
      removed outlier: 3.668A  pdb=" N   LYS A 706 " --> pdb=" O   ARG A 702 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   TYR A 707 " --> pdb=" O   ASN A 703 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   PHE A 708 " --> pdb=" O   LEU A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 716
    Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133
      removed outlier: 7.351A  pdb=" N   GLU A 140 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   VAL A 178 " --> pdb=" O   GLU A 140 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   GLU A 142 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 204
    Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 313
    Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320
    Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 379
      removed outlier: 8.627A  pdb=" N   SER A 448 " --> pdb=" O   SER A 415 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   LEU A 417 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
      removed outlier: 8.224A  pdb=" N   ARG A 450 " --> pdb=" O   LEU A 417 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LEU A 419 " --> pdb=" O   ARG A 450 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   LYS A 452 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   LEU A 421 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   MET A 454 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA7, first strand: chain 'A' and resid 516 through 517
      removed outlier: 5.609A  pdb=" N   TYR A 517 " --> pdb=" O   ALA A 555 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU A 554 " --> pdb=" O   ASP A 610 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU A 609 " --> pdb=" O   THR A 642 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU A 641 " --> pdb=" O   HIS A 678 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 650 through 652

    146 hydrogen bonds defined for protein.
    369 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: 3.58

  Time building geometry restraints manager: 3.27 seconds

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

  Histogram of bond lengths:
        0.91 -     1.08: 1784
        1.08 -     1.26: 3876
        1.26 -     1.44: 1312
        1.44 -     1.62: 2826
        1.62 -     1.80: 6
  Bond restraints: 9804
  Sorted by residual:
  bond pdb=" ND2 ASN A 389 "
       pdb="HD22 ASN A 389 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" NH1 ARG A 316 "
       pdb="HH11 ARG A 316 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" CD2 PHE A 390 "
       pdb=" HD2 PHE A 390 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   TYR A 578 "
       pdb=" H   TYR A 578 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" NH1 ARG A 636 "
       pdb="HH12 ARG A 636 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  ... (remaining 9799 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 15252
        3.05 -     6.09: 1982
        6.09 -     9.14: 432
        9.14 -    12.18: 6
       12.18 -    15.23: 1
  Bond angle restraints: 17673
  Sorted by residual:
  angle pdb=" C   TYR A 284 "
        pdb=" CA  TYR A 284 "
        pdb=" CB  TYR A 284 "
      ideal   model   delta    sigma   weight residual
     109.95  125.18  -15.23 1.99e+00 2.53e-01 5.85e+01
  angle pdb=" CA  ASP A 420 "
        pdb=" CB  ASP A 420 "
        pdb=" CG  ASP A 420 "
      ideal   model   delta    sigma   weight residual
     112.60  119.91   -7.31 1.00e+00 1.00e+00 5.35e+01
  angle pdb=" CA  ASP A 627 "
        pdb=" CB  ASP A 627 "
        pdb=" CG  ASP A 627 "
      ideal   model   delta    sigma   weight residual
     112.60  119.40   -6.80 1.00e+00 1.00e+00 4.63e+01
  angle pdb=" OD1 ASN A 207 "
        pdb=" CG  ASN A 207 "
        pdb=" ND2 ASN A 207 "
      ideal   model   delta    sigma   weight residual
     122.60  116.15    6.45 1.00e+00 1.00e+00 4.16e+01
  angle pdb=" CA  TYR A 284 "
        pdb=" CB  TYR A 284 "
        pdb=" CG  TYR A 284 "
      ideal   model   delta    sigma   weight residual
     113.90  125.29  -11.39 1.80e+00 3.09e-01 4.00e+01
  ... (remaining 17668 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 4135
       17.69 -    35.38: 346
       35.38 -    53.06: 91
       53.06 -    70.75: 40
       70.75 -    88.44: 6
  Dihedral angle restraints: 4618
    sinusoidal: 2535
      harmonic: 2083
  Sorted by residual:
  dihedral pdb=" C   TYR A 284 "
           pdb=" N   TYR A 284 "
           pdb=" CA  TYR A 284 "
           pdb=" CB  TYR A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -142.68   20.08     0      2.50e+00 1.60e-01 6.45e+01
  dihedral pdb=" CA  LYS A 497 "
           pdb=" C   LYS A 497 "
           pdb=" N   ASN A 498 "
           pdb=" CA  ASN A 498 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.49   32.51     0      5.00e+00 4.00e-02 4.23e+01
  dihedral pdb=" CA  SER A 687 "
           pdb=" C   SER A 687 "
           pdb=" N   ILE A 688 "
           pdb=" CA  ILE A 688 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.13   28.87     0      5.00e+00 4.00e-02 3.33e+01
  ... (remaining 4615 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.130: 556
       0.130 -    0.260: 140
       0.260 -    0.390: 17
       0.390 -    0.520: 1
       0.520 -    0.650: 1
  Chirality restraints: 715
  Sorted by residual:
  chirality pdb=" CA  TYR A 284 "
            pdb=" N   TYR A 284 "
            pdb=" C   TYR A 284 "
            pdb=" CB  TYR A 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.06e+01
  chirality pdb=" CA  THR A 486 "
            pdb=" N   THR A 486 "
            pdb=" C   THR A 486 "
            pdb=" CB  THR A 486 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.10    0.42 2.00e-01 2.50e+01 4.44e+00
  chirality pdb=" CA  ASN A 256 "
            pdb=" N   ASN A 256 "
            pdb=" C   ASN A 256 "
            pdb=" CB  ASN A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.64e+00
  ... (remaining 712 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 286 "    0.232 2.00e-02 2.50e+03   1.14e-01 5.19e+02
        pdb=" CG  TRP A 286 "    0.090 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 286 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 286 "    0.055 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 286 "   -0.053 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 286 "    0.058 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 286 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 286 "    0.116 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 286 "   -0.044 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 286 "    0.068 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 286 "   -0.134 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 286 "   -0.176 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 286 "   -0.110 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 286 "    0.114 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 286 "   -0.193 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 286 "    0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 284 "    0.257 2.00e-02 2.50e+03   1.10e-01 3.60e+02
        pdb=" CG  TYR A 284 "   -0.214 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 284 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 284 "   -0.123 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 284 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 284 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 284 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A 284 "    0.063 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 284 "   -0.022 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 284 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 284 "    0.048 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 284 "    0.084 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 515 "   -0.195 2.00e-02 2.50e+03   8.84e-02 3.12e+02
        pdb=" CG  TRP A 515 "   -0.083 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 515 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 515 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 515 "    0.082 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 515 "    0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 515 "    0.058 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 515 "   -0.075 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 515 "    0.052 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 515 "   -0.054 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 515 "    0.040 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 515 "    0.139 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 515 "    0.088 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 515 "   -0.097 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 515 "    0.106 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 515 "   -0.092 2.00e-02 2.50e+03
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 775
        2.21 -     2.81: 17385
        2.81 -     3.40: 26400
        3.40 -     4.00: 34964
        4.00 -     4.60: 50209
  Nonbonded interactions: 129733
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 610 "
            pdb=" HG  SER A 612 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" HG1 THR A 486 "
            pdb=" O   ALA A 514 "
     model   vdw
     1.618 2.450
  nonbonded pdb=" O   LEU A 205 "
            pdb=" HH  TYR A 249 "
     model   vdw
     1.637 2.450
  nonbonded pdb=" HH  TYR A 388 "
            pdb=" OD2 ASP A 442 "
     model   vdw
     1.653 2.450
  nonbonded pdb=" OD1 ASP A 422 "
            pdb=" HG  SER A 424 "
     model   vdw
     1.665 2.450
  ... (remaining 129728 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 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:             1.250
  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:             0.180
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     25.740
  Find NCS groups from input model:        0.070
  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:11.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
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      :  0.014   0.118   5014  Z= 0.831
  Angle     :  1.990  15.226   6760  Z= 1.350
  Chirality :  0.113   0.650    715
  Planarity :  0.015   0.128    896
  Dihedral  : 14.683  88.439   1912
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 0.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  6.80 %
    Favored  : 93.01 %
  Cbeta Deviations :  0.70 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.31), residues: 611
  helix: -3.22 (0.26), residues: 155
  sheet:  0.05 (0.61), residues: 62
  loop : -0.92 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.123   0.033   TRP A 286 
 HIS   0.016   0.007   HIS A 664 
 PHE   0.047   0.011   PHE A 206 
 TYR   0.246   0.021   TYR A 284 
 ARG   0.008   0.002   ARG A 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24015 (  146)
  hydrogen bonds       : angle       8.59248 (  369)
  covalent geometry    : bond        0.01363 ( 5014)
  covalent geometry    : angle       1.99000 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.794 
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
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8037 (mttt)
REVERT: A  174 LYS cc_start: 0.7867 (tptt) cc_final: 0.7108 (ttpt)
REVERT: A  222 LYS cc_start: 0.7381 (mttt) cc_final: 0.6819 (mtpt)
REVERT: A  276 LYS cc_start: 0.7332 (mmmm) cc_final: 0.7058 (ttpp)
REVERT: A  305 LYS cc_start: 0.6252 (pttp) cc_final: 0.6043 (mtmm)
REVERT: A  391 LYS cc_start: 0.7318 (mtmm) cc_final: 0.7091 (mtmm)
REVERT: A  399 SER cc_start: 0.8142 (p) cc_final: 0.7743 (m)
REVERT: A  472 LYS cc_start: 0.6988 (ttpt) cc_final: 0.6650 (ttmm)
REVERT: A  475 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6728 (mm110)
REVERT: A  523 ARG cc_start: 0.6911 (ttm-80) cc_final: 0.6591 (ttm-80)
REVERT: A  634 GLU cc_start: 0.6888 (tt0) cc_final: 0.6312 (tm-30)
REVERT: A  640 GLU cc_start: 0.7277 (tt0) cc_final: 0.6872 (mp0)
REVERT: A  647 GLU cc_start: 0.6924 (mp0) cc_final: 0.6602 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 119
  average time/residue: 2.6363
  time to fit residues: 325.2263
Evaluate side-chains
  82 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  671 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 260 ASN
A 369 ASN
A 440 GLN
A 458 ASN
A 461 GLN
A 529 ASN
A 581 ASN
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 671 ASN
A 711 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.213475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.190540 restraints weight = 15168.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.4219 rms_B_bonded: 1.80
r_work: 0.4121 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4002 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5014  Z= 0.140
  Angle     :  0.630   8.425   6760  Z= 0.345
  Chirality :  0.044   0.206    715
  Planarity :  0.004   0.031    896
  Dihedral  :  6.985  39.764    672
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.79 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.32), residues: 611
  helix: -1.76 (0.33), residues: 174
  sheet:  0.18 (0.59), residues: 64
  loop : -1.02 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 286 
 HIS   0.004   0.002   HIS A 170 
 PHE   0.013   0.001   PHE A 390 
 TYR   0.053   0.002   TYR A 284 
 ARG   0.003   0.001   ARG A 450 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04194 (  146)
  hydrogen bonds       : angle       5.79311 (  369)
  covalent geometry    : bond        0.00319 ( 5014)
  covalent geometry    : angle       0.63010 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LYS cc_start: 0.7984 (tptt) cc_final: 0.7531 (ttpt)
REVERT: A  222 LYS cc_start: 0.7668 (mttt) cc_final: 0.7112 (mtpt)
REVERT: A  232 GLU cc_start: 0.4236 (tt0) cc_final: 0.4032 (mt-10)
REVERT: A  284 TYR cc_start: 0.5750 (OUTLIER) cc_final: 0.5483 (p90)
REVERT: A  305 LYS cc_start: 0.7159 (pttp) cc_final: 0.6642 (mtmm)
REVERT: A  309 LYS cc_start: 0.6316 (mtpt) cc_final: 0.5815 (mppt)
REVERT: A  397 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.5677 (mtm-85)
REVERT: A  405 ASN cc_start: 0.7976 (m-40) cc_final: 0.7767 (m110)
REVERT: A  441 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7469 (pttm)
REVERT: A  472 LYS cc_start: 0.7482 (ttpt) cc_final: 0.7225 (ttmm)
REVERT: A  617 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7579 (pp)
REVERT: A  647 GLU cc_start: 0.7389 (mp0) cc_final: 0.7157 (mp0)
  outliers start: 15
  outliers final: 2
  residues processed: 97
  average time/residue: 2.8293
  time to fit residues: 284.6523
Evaluate side-chains
  77 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  397 ARG
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  617 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0070
   chunk 18 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.2004

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

Flipped N/Q/H residues before XYZ refinement:
A 197 ASN
A 445 GLN
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN
A 658 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.209854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.185985 restraints weight = 15436.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.4178 rms_B_bonded: 1.86
r_work: 0.4079 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3959 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5014  Z= 0.126
  Angle     :  0.571   8.475   6760  Z= 0.310
  Chirality :  0.042   0.204    715
  Planarity :  0.004   0.031    896
  Dihedral  :  5.991  29.532    670
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.01 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.33), residues: 611
  helix: -1.11 (0.36), residues: 174
  sheet:  0.66 (0.67), residues: 58
  loop : -1.18 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 286 
 HIS   0.004   0.001   HIS A 170 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.056   0.002   TYR A 284 
 ARG   0.002   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03663 (  146)
  hydrogen bonds       : angle       5.27261 (  369)
  covalent geometry    : bond        0.00292 ( 5014)
  covalent geometry    : angle       0.57088 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  86 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LYS cc_start: 0.7943 (tptt) cc_final: 0.7448 (ttpt)
REVERT: A  222 LYS cc_start: 0.7710 (mttt) cc_final: 0.7170 (mtmt)
REVERT: A  268 LYS cc_start: 0.7572 (mmmt) cc_final: 0.7255 (mtmt)
REVERT: A  305 LYS cc_start: 0.7128 (pttp) cc_final: 0.6593 (mtmm)
REVERT: A  309 LYS cc_start: 0.6449 (mtpt) cc_final: 0.5882 (mppt)
REVERT: A  397 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.5732 (mtm-85)
REVERT: A  472 LYS cc_start: 0.7407 (ttpt) cc_final: 0.7113 (ttmm)
REVERT: A  617 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7539 (pp)
REVERT: A  640 GLU cc_start: 0.8340 (tt0) cc_final: 0.8031 (mm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 79
  average time/residue: 2.7622
  time to fit residues: 226.5706
Evaluate side-chains
  76 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 ASN
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  397 ARG
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  634 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 587 GLN
A 671 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.208761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.184775 restraints weight = 15335.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.4165 rms_B_bonded: 1.86
r_work: 0.4066 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3947 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5014  Z= 0.135
  Angle     :  0.556   9.034   6760  Z= 0.303
  Chirality :  0.042   0.191    715
  Planarity :  0.004   0.032    896
  Dihedral  :  5.779  28.797    670
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.30 %
    Favored  : 78.86 %
  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: -1.31 (0.33), residues: 611
  helix: -0.77 (0.38), residues: 172
  sheet:  0.75 (0.68), residues: 58
  loop : -1.20 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 286 
 HIS   0.004   0.001   HIS A 170 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.046   0.002   TYR A 284 
 ARG   0.003   0.000   ARG A 613 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  146)
  hydrogen bonds       : angle       5.11527 (  369)
  covalent geometry    : bond        0.00308 ( 5014)
  covalent geometry    : angle       0.55619 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  83 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 LYS cc_start: 0.7911 (tptt) cc_final: 0.7485 (ttpt)
REVERT: A  222 LYS cc_start: 0.7716 (mttt) cc_final: 0.7131 (mtmt)
REVERT: A  268 LYS cc_start: 0.7557 (mmmt) cc_final: 0.7314 (mtmt)
REVERT: A  284 TYR cc_start: 0.5622 (OUTLIER) cc_final: 0.5154 (p90)
REVERT: A  305 LYS cc_start: 0.7186 (pttp) cc_final: 0.6658 (mtmm)
REVERT: A  309 LYS cc_start: 0.6498 (mtpt) cc_final: 0.5935 (mppt)
REVERT: A  472 LYS cc_start: 0.7405 (ttpt) cc_final: 0.7084 (ttmm)
REVERT: A  617 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7601 (pp)
REVERT: A  640 GLU cc_start: 0.8317 (tt0) cc_final: 0.8044 (mm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 78
  average time/residue: 2.5738
  time to fit residues: 208.7695
Evaluate side-chains
  73 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  634 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 28 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
A 563 ASN
A 590 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.208735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.184812 restraints weight = 15355.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.4169 rms_B_bonded: 1.85
r_work: 0.4070 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3949 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5014  Z= 0.120
  Angle     :  0.549   9.605   6760  Z= 0.290
  Chirality :  0.041   0.189    715
  Planarity :  0.004   0.030    896
  Dihedral  :  5.417  28.098    670
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.93 %
    Favored  : 78.12 %
  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: -1.21 (0.33), residues: 611
  helix: -0.33 (0.40), residues: 167
  sheet:  0.87 (0.70), residues: 58
  loop : -1.34 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 286 
 HIS   0.005   0.001   HIS A 590 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.043   0.001   TYR A 284 
 ARG   0.002   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03196 (  146)
  hydrogen bonds       : angle       4.90693 (  369)
  covalent geometry    : bond        0.00273 ( 5014)
  covalent geometry    : angle       0.54851 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LYS cc_start: 0.7873 (tptt) cc_final: 0.7506 (ttmm)
REVERT: A  222 LYS cc_start: 0.7699 (mttt) cc_final: 0.7145 (mtmt)
REVERT: A  268 LYS cc_start: 0.7578 (mmmt) cc_final: 0.7325 (mtmt)
REVERT: A  283 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6411 (tp30)
REVERT: A  284 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.5036 (p90)
REVERT: A  305 LYS cc_start: 0.7157 (pttp) cc_final: 0.6580 (mtmm)
REVERT: A  309 LYS cc_start: 0.6482 (mtpt) cc_final: 0.5885 (mppt)
REVERT: A  472 LYS cc_start: 0.7326 (ttpt) cc_final: 0.6993 (tppt)
REVERT: A  498 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7013 (t0)
REVERT: A  617 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7558 (pp)
REVERT: A  640 GLU cc_start: 0.8312 (tt0) cc_final: 0.8045 (mm-30)
REVERT: A  701 ARG cc_start: 0.5693 (mtt90) cc_final: 0.5492 (ttt90)
  outliers start: 16
  outliers final: 6
  residues processed: 77
  average time/residue: 2.3502
  time to fit residues: 189.0187
Evaluate side-chains
  76 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  283 GLU
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  498 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain A residue  734 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 563 ASN
A 590 HIS
A 645 ASN
A 684 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.205492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.181755 restraints weight = 15448.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 1.84
r_work: 0.4036 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3922 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5014  Z= 0.161
  Angle     :  0.562   9.139   6760  Z= 0.305
  Chirality :  0.042   0.196    715
  Planarity :  0.004   0.031    896
  Dihedral  :  5.577  28.978    670
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 18.93 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.32), residues: 611
  helix: -0.34 (0.39), residues: 167
  sheet:  0.93 (0.70), residues: 58
  loop : -1.50 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 515 
 HIS   0.004   0.002   HIS A 590 
 PHE   0.013   0.001   PHE A 586 
 TYR   0.049   0.002   TYR A 284 
 ARG   0.002   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03682 (  146)
  hydrogen bonds       : angle       4.96760 (  369)
  covalent geometry    : bond        0.00371 ( 5014)
  covalent geometry    : angle       0.56180 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.823 
Fit side-chains
REVERT: A  174 LYS cc_start: 0.7880 (tptt) cc_final: 0.7527 (ttmm)
REVERT: A  222 LYS cc_start: 0.7794 (mttt) cc_final: 0.7208 (mtpt)
REVERT: A  274 LYS cc_start: 0.7065 (tptm) cc_final: 0.6844 (tptt)
REVERT: A  280 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6722 (mmtm)
REVERT: A  283 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6724 (tp30)
REVERT: A  284 TYR cc_start: 0.5612 (OUTLIER) cc_final: 0.5105 (p90)
REVERT: A  305 LYS cc_start: 0.7112 (pttp) cc_final: 0.6873 (ptpp)
REVERT: A  309 LYS cc_start: 0.6545 (mtpt) cc_final: 0.6003 (mppt)
REVERT: A  386 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7459 (tttt)
REVERT: A  472 LYS cc_start: 0.7320 (ttpt) cc_final: 0.6976 (tppt)
REVERT: A  498 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7152 (t0)
REVERT: A  542 HIS cc_start: 0.6364 (t70) cc_final: 0.5902 (m90)
REVERT: A  617 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7599 (pp)
REVERT: A  640 GLU cc_start: 0.8336 (tt0) cc_final: 0.7993 (mt-10)
REVERT: A  671 ASN cc_start: 0.7740 (m-40) cc_final: 0.7504 (t0)
  outliers start: 20
  outliers final: 8
  residues processed: 86
  average time/residue: 2.2921
  time to fit residues: 206.3686
Evaluate side-chains
  84 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  283 GLU
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  498 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  734 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
A 563 ASN
A 590 HIS
A 684 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.204962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.181348 restraints weight = 15635.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 1.83
r_work: 0.4026 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3908 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.4816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5014  Z= 0.182
  Angle     :  0.593  10.123   6760  Z= 0.318
  Chirality :  0.042   0.202    715
  Planarity :  0.004   0.034    896
  Dihedral  :  5.715  29.922    670
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.49 %
    Favored  : 76.65 %
  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: -1.51 (0.32), residues: 611
  helix: -0.53 (0.38), residues: 173
  sheet:  0.97 (0.70), residues: 58
  loop : -1.62 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 286 
 HIS   0.004   0.002   HIS A 590 
 PHE   0.014   0.002   PHE A 586 
 TYR   0.054   0.002   TYR A 284 
 ARG   0.002   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  146)
  hydrogen bonds       : angle       5.02980 (  369)
  covalent geometry    : bond        0.00421 ( 5014)
  covalent geometry    : angle       0.59253 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  97 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 LYS cc_start: 0.7861 (tptt) cc_final: 0.7489 (ttmm)
REVERT: A  222 LYS cc_start: 0.7793 (mttt) cc_final: 0.7173 (mtpt)
REVERT: A  268 LYS cc_start: 0.7634 (mmmt) cc_final: 0.7347 (mtmt)
REVERT: A  274 LYS cc_start: 0.7148 (tptm) cc_final: 0.6899 (tptt)
REVERT: A  283 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6663 (tp30)
REVERT: A  284 TYR cc_start: 0.5763 (OUTLIER) cc_final: 0.5257 (p90)
REVERT: A  305 LYS cc_start: 0.7030 (pttp) cc_final: 0.6775 (ptpp)
REVERT: A  309 LYS cc_start: 0.6452 (mtpt) cc_final: 0.5921 (mppt)
REVERT: A  386 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7441 (tttt)
REVERT: A  472 LYS cc_start: 0.7332 (ttpt) cc_final: 0.6936 (tppt)
REVERT: A  498 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7132 (t0)
REVERT: A  501 GLU cc_start: 0.6717 (tp30) cc_final: 0.6463 (tm-30)
REVERT: A  617 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7590 (pp)
REVERT: A  640 GLU cc_start: 0.8374 (tt0) cc_final: 0.8071 (mm-30)
  outliers start: 21
  outliers final: 7
  residues processed: 88
  average time/residue: 2.2627
  time to fit residues: 208.3037
Evaluate side-chains
  85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 GLU
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  498 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  734 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 563 ASN
A 590 HIS
A 684 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.205926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.182219 restraints weight = 15604.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 1.85
r_work: 0.4039 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3919 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.4905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5014  Z= 0.145
  Angle     :  0.564  10.212   6760  Z= 0.301
  Chirality :  0.041   0.191    715
  Planarity :  0.004   0.034    896
  Dihedral  :  5.513  29.178    670
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.12 %
    Favored  : 77.21 %
  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: -1.42 (0.32), residues: 611
  helix: -0.22 (0.40), residues: 167
  sheet:  0.95 (0.70), residues: 58
  loop : -1.67 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 286 
 HIS   0.004   0.001   HIS A 590 
 PHE   0.011   0.001   PHE A 390 
 TYR   0.050   0.002   TYR A 284 
 ARG   0.002   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  146)
  hydrogen bonds       : angle       4.88042 (  369)
  covalent geometry    : bond        0.00336 ( 5014)
  covalent geometry    : angle       0.56351 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 LYS cc_start: 0.7847 (tptt) cc_final: 0.7480 (ttmm)
REVERT: A  222 LYS cc_start: 0.7716 (mttt) cc_final: 0.7104 (mtpt)
REVERT: A  268 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7305 (mtmt)
REVERT: A  283 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6487 (tp30)
REVERT: A  284 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.5115 (p90)
REVERT: A  305 LYS cc_start: 0.7065 (pttp) cc_final: 0.6817 (ptpp)
REVERT: A  309 LYS cc_start: 0.6430 (mtpt) cc_final: 0.5919 (mppt)
REVERT: A  386 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7424 (tttt)
REVERT: A  420 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.5938 (m-30)
REVERT: A  472 LYS cc_start: 0.7302 (ttpt) cc_final: 0.6894 (tppt)
REVERT: A  498 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7245 (t0)
REVERT: A  501 GLU cc_start: 0.6683 (tp30) cc_final: 0.6367 (tm-30)
REVERT: A  617 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7593 (pp)
REVERT: A  640 GLU cc_start: 0.8398 (tt0) cc_final: 0.8089 (mm-30)
REVERT: A  671 ASN cc_start: 0.7902 (m-40) cc_final: 0.7661 (t0)
  outliers start: 20
  outliers final: 6
  residues processed: 89
  average time/residue: 2.4514
  time to fit residues: 228.2864
Evaluate side-chains
  84 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 GLU
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  498 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  734 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
A 563 ASN
A 590 HIS
A 684 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.206627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.183476 restraints weight = 15530.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 1.81
r_work: 0.4056 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3941 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.4975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5014  Z= 0.125
  Angle     :  0.551   8.770   6760  Z= 0.295
  Chirality :  0.041   0.186    715
  Planarity :  0.004   0.032    896
  Dihedral  :  5.347  28.448    670
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.40 %
    Favored  : 77.02 %
  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: -1.33 (0.32), residues: 611
  helix: -0.09 (0.40), residues: 168
  sheet:  0.98 (0.71), residues: 58
  loop : -1.63 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 286 
 HIS   0.005   0.001   HIS A 590 
 PHE   0.011   0.001   PHE A 390 
 TYR   0.049   0.001   TYR A 284 
 ARG   0.002   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  146)
  hydrogen bonds       : angle       4.76710 (  369)
  covalent geometry    : bond        0.00293 ( 5014)
  covalent geometry    : angle       0.55127 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  86 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 LYS cc_start: 0.7861 (tptt) cc_final: 0.7540 (ttmm)
REVERT: A  222 LYS cc_start: 0.7709 (mttt) cc_final: 0.7110 (mtpt)
REVERT: A  268 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7374 (mtmt)
REVERT: A  283 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6556 (tp30)
REVERT: A  284 TYR cc_start: 0.5466 (OUTLIER) cc_final: 0.4941 (p90)
REVERT: A  305 LYS cc_start: 0.7088 (pttp) cc_final: 0.6834 (ptpp)
REVERT: A  309 LYS cc_start: 0.6425 (mtpt) cc_final: 0.5888 (mppt)
REVERT: A  386 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7435 (tttt)
REVERT: A  472 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6885 (tppt)
REVERT: A  498 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7249 (t0)
REVERT: A  501 GLU cc_start: 0.6691 (tp30) cc_final: 0.6403 (tm-30)
REVERT: A  617 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7600 (pp)
REVERT: A  640 GLU cc_start: 0.8366 (tt0) cc_final: 0.8061 (mm-30)
REVERT: A  671 ASN cc_start: 0.7841 (m-40) cc_final: 0.7635 (t0)
  outliers start: 14
  outliers final: 4
  residues processed: 80
  average time/residue: 2.4323
  time to fit residues: 203.0449
Evaluate side-chains
  79 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 GLU
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  498 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain A residue  734 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 563 ASN
A 590 HIS
A 684 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.206135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.182946 restraints weight = 15566.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.4147 rms_B_bonded: 1.81
r_work: 0.4046 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3930 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.5003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5014  Z= 0.134
  Angle     :  0.552   9.958   6760  Z= 0.294
  Chirality :  0.041   0.188    715
  Planarity :  0.004   0.032    896
  Dihedral  :  5.340  28.495    670
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.40 %
    Favored  : 77.02 %
  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: -1.30 (0.32), residues: 611
  helix: -0.04 (0.41), residues: 167
  sheet:  1.01 (0.72), residues: 58
  loop : -1.63 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 286 
 HIS   0.006   0.002   HIS A 590 
 PHE   0.011   0.001   PHE A 390 
 TYR   0.049   0.002   TYR A 284 
 ARG   0.002   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03239 (  146)
  hydrogen bonds       : angle       4.74305 (  369)
  covalent geometry    : bond        0.00310 ( 5014)
  covalent geometry    : angle       0.55203 ( 6760)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 LYS cc_start: 0.7856 (tptt) cc_final: 0.7523 (ttmm)
REVERT: A  183 LYS cc_start: 0.6917 (mtpm) cc_final: 0.6591 (mppt)
REVERT: A  222 LYS cc_start: 0.7706 (mttt) cc_final: 0.7075 (mtpt)
REVERT: A  268 LYS cc_start: 0.7640 (mmmt) cc_final: 0.7351 (mtmt)
REVERT: A  283 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6588 (tp30)
REVERT: A  284 TYR cc_start: 0.5477 (OUTLIER) cc_final: 0.4934 (p90)
REVERT: A  305 LYS cc_start: 0.7078 (pttp) cc_final: 0.6837 (ptpp)
REVERT: A  309 LYS cc_start: 0.6440 (mtpt) cc_final: 0.5885 (mppt)
REVERT: A  386 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7417 (tttt)
REVERT: A  472 LYS cc_start: 0.7290 (ttpt) cc_final: 0.6969 (tppt)
REVERT: A  475 GLN cc_start: 0.7304 (mm110) cc_final: 0.6909 (mm110)
REVERT: A  617 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7598 (pp)
REVERT: A  640 GLU cc_start: 0.8386 (tt0) cc_final: 0.8085 (mm-30)
REVERT: A  671 ASN cc_start: 0.7838 (m-40) cc_final: 0.7635 (t0)
  outliers start: 14
  outliers final: 5
  residues processed: 78
  average time/residue: 2.3980
  time to fit residues: 195.2212
Evaluate side-chains
  77 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 GLU
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain A residue  734 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    0.1980
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
A 563 ASN
A 590 HIS
A 684 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.205740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.182626 restraints weight = 15513.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 1.80
r_work: 0.4044 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3924 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.5054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5014  Z= 0.141
  Angle     :  0.566  10.179   6760  Z= 0.302
  Chirality :  0.041   0.190    715
  Planarity :  0.004   0.032    896
  Dihedral  :  5.332  28.769    670
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.59 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.32), residues: 611
  helix: -0.06 (0.40), residues: 167
  sheet:  1.05 (0.71), residues: 58
  loop : -1.61 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 286 
 HIS   0.002   0.001   HIS A 170 
 PHE   0.011   0.001   PHE A 390 
 TYR   0.048   0.002   TYR A 284 
 ARG   0.002   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03245 (  146)
  hydrogen bonds       : angle       4.72977 (  369)
  covalent geometry    : bond        0.00328 ( 5014)
  covalent geometry    : angle       0.56631 ( 6760)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8868.73 seconds
wall clock time: 152 minutes 38.76 seconds (9158.76 seconds total)