Starting phenix.real_space_refine
on Tue Feb 11 14:01:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wm9_37646/02_2025/8wm9_37646_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wm9_37646/02_2025/8wm9_37646.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wm9_37646/02_2025/8wm9_37646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wm9_37646/02_2025/8wm9_37646.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wm9_37646/02_2025/8wm9_37646_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wm9_37646/02_2025/8wm9_37646_neut.cif"
  }
  resolution = 3.53
  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=   0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    3958      2.51       5
     N     884      2.21       5
     O     999      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5879
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 320, 2492
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 313}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 47
    Chain: "B"
      Number of atoms: 2377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2377
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 303}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 160
          Unresolved non-hydrogen dihedrals: 105
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 82
    Chain: "C"
      Number of atoms: 660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 660
          Classifications: {'peptide': 89}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "A"
      Number of atoms: 175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 175
          Unusual residues: {'Y01': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 175
          Unusual residues: {'Y01': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 4.30, per 1000 atoms: 0.73
  Number of scatterers: 5879
  At special positions: 0
  Unit cell: (90.2, 94.6, 90.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O     999      8.00
     N     884      7.00
     C    3958      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 204 " - pdb=" SG  CYS A 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 302 " - pdb=" SG  CYS A 377 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 204 " - pdb=" SG  CYS B 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 302 " - pdb=" SG  CYS B 377 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 840.7 milliseconds
  

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1360

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      72.9% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 212 through 244
      removed outlier: 3.890A  pdb=" N   ASP A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 276
      removed outlier: 3.886A  pdb=" N   PHE A 257 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA A 268 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TYR A 269 " --> pdb=" O   TYR A 265 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 281
      removed outlier: 3.568A  pdb=" N   ILE A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 298
    Processing helix  chain 'A' and resid 299 through 332
      removed outlier: 3.510A  pdb=" N   ALA A 303 " --> pdb=" O   ASN A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 342
      No H-bonds generated for 'chain 'A' and resid 340 through 342'
    Processing helix  chain 'A' and resid 343 through 366
      removed outlier: 3.771A  pdb=" N   PHE A 347 " --> pdb=" O   HIS A 343 " (cutoff:3.500A)
      Proline residue:  A 355  - end of helix
    Processing helix  chain 'A' and resid 383 through 391
      removed outlier: 3.686A  pdb=" N   VAL A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 421
      removed outlier: 3.530A  pdb=" N   LEU A 395 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 461
      removed outlier: 3.969A  pdb=" N   GLU A 431 " --> pdb=" O   THR A 427 " (cutoff:3.500A)
      Proline residue:  A 447  - end of helix
    Processing helix  chain 'A' and resid 462 through 465
    Processing helix  chain 'A' and resid 471 through 490
      removed outlier: 3.503A  pdb=" N   ALA A 475 " --> pdb=" O   ASP A 471 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   GLY A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 496
      removed outlier: 3.516A  pdb=" N   TRP A 496 " --> pdb=" O   MET A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 511
      removed outlier: 3.870A  pdb=" N   LEU A 511 " --> pdb=" O   PHE A 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 244
      removed outlier: 3.846A  pdb=" N   LYS B 216 " --> pdb=" O   SER B 212 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASP B 244 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 248
    Processing helix  chain 'B' and resid 253 through 276
      removed outlier: 3.675A  pdb=" N   PHE B 257 " --> pdb=" O   ARG B 253 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA B 268 " --> pdb=" O   ILE B 264 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   TYR B 269 " --> pdb=" O   TYR B 265 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE B 270 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ARG B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 281
      removed outlier: 3.647A  pdb=" N   ILE B 280 " --> pdb=" O   GLY B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 332
      removed outlier: 3.633A  pdb=" N   ALA B 303 " --> pdb=" O   ASN B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 342
      removed outlier: 3.595A  pdb=" N   ILE B 340 " --> pdb=" O   GLY B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 366
      removed outlier: 3.696A  pdb=" N   PHE B 347 " --> pdb=" O   HIS B 343 " (cutoff:3.500A)
      Proline residue:  B 355  - end of helix
      removed outlier: 3.635A  pdb=" N   MET B 365 " --> pdb=" O   VAL B 361 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ARG B 366 " --> pdb=" O   ILE B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 391
    Processing helix  chain 'B' and resid 391 through 418
    Processing helix  chain 'B' and resid 432 through 461
      removed outlier: 4.047A  pdb=" N   VAL B 446 " --> pdb=" O   VAL B 442 " (cutoff:3.500A)
      Proline residue:  B 447  - end of helix
    Processing helix  chain 'B' and resid 461 through 468
      removed outlier: 3.520A  pdb=" N   TYR B 467 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 490
      removed outlier: 3.842A  pdb=" N   ALA B 475 " --> pdb=" O   ASP B 471 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   VAL B 487 " --> pdb=" O   MET B 483 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   GLY B 488 " --> pdb=" O   SER B 484 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE B 489 " --> pdb=" O   LEU B 485 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   THR B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 513
      removed outlier: 3.639A  pdb=" N   LEU B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 431
    Processing helix  chain 'C' and resid 455 through 465
    Processing helix  chain 'C' and resid 474 through 485
      removed outlier: 3.748A  pdb=" N   TYR C 478 " --> pdb=" O   GLU C 474 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   SER C 480 " --> pdb=" O   ARG C 476 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 193
    Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 370
    Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 370
    Processing sheet with id=AA4, first strand: chain 'C' and resid 440 through 444
      removed outlier: 6.750A  pdb=" N   ARG C 442 " --> pdb=" O   PRO C 450 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   TRP C 444 " --> pdb=" O   THR C 448 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   THR C 448 " --> pdb=" O   TRP C 444 " (cutoff:3.500A)

    367 hydrogen bonds defined for protein.
    1083 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.43

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1679
        1.34 -     1.46: 1562
        1.46 -     1.58: 2749
        1.58 -     1.71: 1
        1.71 -     1.83: 60
  Bond restraints: 6051
  Sorted by residual:
  bond pdb=" CAV Y01 B 603 "
       pdb=" CAZ Y01 B 603 "
    ideal  model  delta    sigma   weight residual
    1.507  1.450  0.057 2.00e-02 2.50e+03 8.00e+00
  bond pdb=" CBB Y01 B 603 "
       pdb=" CBE Y01 B 603 "
    ideal  model  delta    sigma   weight residual
    1.535  1.591 -0.056 2.00e-02 2.50e+03 7.86e+00
  bond pdb=" CAV Y01 B 603 "
       pdb=" CBC Y01 B 603 "
    ideal  model  delta    sigma   weight residual
    1.523  1.467  0.056 2.00e-02 2.50e+03 7.83e+00
  bond pdb=" CAY Y01 B 605 "
       pdb=" OAW Y01 B 605 "
    ideal  model  delta    sigma   weight residual
    1.332  1.382 -0.050 2.00e-02 2.50e+03 6.18e+00
  bond pdb=" CAZ Y01 B 604 "
       pdb=" CBH Y01 B 604 "
    ideal  model  delta    sigma   weight residual
    1.519  1.470  0.049 2.00e-02 2.50e+03 5.92e+00
  ... (remaining 6046 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 7855
        1.70 -     3.40: 310
        3.40 -     5.10: 92
        5.10 -     6.81: 40
        6.81 -     8.51: 6
  Bond angle restraints: 8303
  Sorted by residual:
  angle pdb=" N   TYR A 206 "
        pdb=" CA  TYR A 206 "
        pdb=" C   TYR A 206 "
      ideal   model   delta    sigma   weight residual
     111.02  107.35    3.67 1.22e+00 6.72e-01 9.05e+00
  angle pdb=" CAJ Y01 B 603 "
        pdb=" CAO Y01 B 603 "
        pdb=" CBB Y01 B 603 "
      ideal   model   delta    sigma   weight residual
     115.08  106.57    8.51 3.00e+00 1.11e-01 8.04e+00
  angle pdb=" C   TYR B 250 "
        pdb=" CA  TYR B 250 "
        pdb=" CB  TYR B 250 "
      ideal   model   delta    sigma   weight residual
     109.46  113.98   -4.52 1.64e+00 3.72e-01 7.60e+00
  angle pdb=" CAL Y01 B 604 "
        pdb=" CAM Y01 B 604 "
        pdb=" CAY Y01 B 604 "
      ideal   model   delta    sigma   weight residual
     113.76  105.85    7.91 3.00e+00 1.11e-01 6.95e+00
  angle pdb=" N   ASP A 207 "
        pdb=" CA  ASP A 207 "
        pdb=" C   ASP A 207 "
      ideal   model   delta    sigma   weight residual
     109.62  105.72    3.90 1.50e+00 4.44e-01 6.76e+00
  ... (remaining 8298 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 3604
       17.48 -    34.96: 290
       34.96 -    52.45: 48
       52.45 -    69.93: 14
       69.93 -    87.41: 3
  Dihedral angle restraints: 3959
    sinusoidal: 1855
      harmonic: 2104
  Sorted by residual:
  dihedral pdb=" CB  CYS B 302 "
           pdb=" SG  CYS B 302 "
           pdb=" SG  CYS B 377 "
           pdb=" CB  CYS B 377 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.72   61.28     1      1.00e+01 1.00e-02 4.99e+01
  dihedral pdb=" CB  CYS A 302 "
           pdb=" SG  CYS A 302 "
           pdb=" SG  CYS A 377 "
           pdb=" CB  CYS A 377 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.54   51.46     1      1.00e+01 1.00e-02 3.62e+01
  dihedral pdb=" CA  MET C 430 "
           pdb=" C   MET C 430 "
           pdb=" N   ALA C 431 "
           pdb=" CA  ALA C 431 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.00  -20.00     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 3956 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 829
       0.064 -    0.129: 111
       0.129 -    0.193: 20
       0.193 -    0.257: 17
       0.257 -    0.321: 12
  Chirality restraints: 989
  Sorted by residual:
  chirality pdb=" CBG Y01 B 603 "
            pdb=" CAQ Y01 B 603 "
            pdb=" CBD Y01 B 603 "
            pdb=" CBI Y01 B 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.65    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CBG Y01 A 605 "
            pdb=" CAQ Y01 A 605 "
            pdb=" CBD Y01 A 605 "
            pdb=" CBI Y01 A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.64    0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CBG Y01 B 604 "
            pdb=" CAQ Y01 B 604 "
            pdb=" CBD Y01 B 604 "
            pdb=" CBI Y01 B 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.63    0.30 2.00e-01 2.50e+01 2.25e+00
  ... (remaining 986 not shown)

  Planarity restraints: 949
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 259 "   -0.010 2.00e-02 2.50e+03   2.06e-02 4.24e+00
        pdb=" C   SER A 259 "    0.036 2.00e-02 2.50e+03
        pdb=" O   SER A 259 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   MET A 260 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 253 "    0.032 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO A 254 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 254 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 254 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 260 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.08e+00
        pdb=" C   MET A 260 "    0.030 2.00e-02 2.50e+03
        pdb=" O   MET A 260 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   CYS A 261 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 946 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 288
        2.73 -     3.27: 6249
        3.27 -     3.81: 9332
        3.81 -     4.36: 10261
        4.36 -     4.90: 17713
  Nonbonded interactions: 43843
  Sorted by model distance:
  nonbonded pdb=" O   THR A 237 "
            pdb=" OG1 THR A 240 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" O   ILE A 256 "
            pdb=" OG  SER A 259 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   LYS B 216 "
            pdb=" OG1 THR B 219 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   ARG C 476 "
            pdb=" OG  SER C 480 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   THR A 445 "
            pdb=" OG1 THR A 449 "
     model   vdw
     2.320 3.040
  ... (remaining 43838 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 188 through 189 or (resid 190 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 191 through 193 or (resid 194 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 195 through 197 or (resid  \ 
198 through 199 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 200 or resid 205 or (resid 206 through 208 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 209 or (resid 210 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 211 through 277 or (resid 278 through 279 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 280 through 293 o \ 
r (resid 294 through 295 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 296 through 333 or (resid 334 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 335 through 371 or (resid 372 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 373 through 409 or (resid 410 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 411 through 412 or (r \ 
esid 413 through 414 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 415 or (resid 416 through 417 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 418 through 421 or (resid 430 through 432 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 433 through 466 or (resid 467 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 468 through 4 \ 
69 or (resid 470 and (name N or name CA or name C or name O or name CB )) or res \ 
id 471 through 493 or (resid 494 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 495 through 501 or (resid 502 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 503 through 510 or (resid 511 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 512 through 513 or resid 601  \ 
through 605))
  selection = (chain 'B' and (resid 188 through 195 or (resid 196 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 197 through 198 or (resid 199 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 204 through 278 or (resid  \ 
279 and (name N or name CA or name C or name O or name CB )) or resid 280 throug \ 
h 282 or (resid 289 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 290 or (resid 291 through 292 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 293 through 507 or (resid 508 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 509 or (resid 510 through 511 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 512 through 513 or resid 6 \ 
01 through 605))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.260
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
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      :  0.006   0.057   6051  Z= 0.408
  Angle     :  0.912   8.508   8303  Z= 0.422
  Chirality :  0.063   0.321    989
  Planarity :  0.005   0.047    949
  Dihedral  : 12.827  87.412   2587
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -0.64 (0.29), residues: 705
  helix:  0.62 (0.22), residues: 463
  sheet: -4.29 (1.48), residues: 10
  loop : -2.39 (0.34), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 222 
 HIS   0.005   0.001   HIS B 348 
 PHE   0.020   0.002   PHE B 482 
 TYR   0.023   0.002   TYR B 262 
 ARG   0.003   0.000   ARG B 247 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
REVERT: A  349 ILE cc_start: 0.8149 (mt) cc_final: 0.7894 (mt)
REVERT: A  434 MET cc_start: 0.5923 (mtm) cc_final: 0.5673 (mtm)
REVERT: A  444 TYR cc_start: 0.8248 (t80) cc_final: 0.7688 (t80)
REVERT: B  222 TRP cc_start: 0.6859 (t-100) cc_final: 0.6477 (t-100)
REVERT: B  382 GLN cc_start: 0.7703 (mm110) cc_final: 0.7311 (mp10)
REVERT: B  436 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7647 (tmmt)
REVERT: C  493 ASN cc_start: 0.8227 (m-40) cc_final: 0.8024 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1584
  time to fit residues: 27.4416
Evaluate side-chains
  120 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0270
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:   20.0000
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.7042

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.168198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.134605 restraints weight = 8877.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.138168 restraints weight = 5317.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.140035 restraints weight = 3852.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6051  Z= 0.278
  Angle     :  0.613   7.392   8303  Z= 0.315
  Chirality :  0.043   0.285    989
  Planarity :  0.004   0.047    949
  Dihedral  :  8.757  59.749   1477
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  7.68 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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:  0.10 (0.31), residues: 705
  helix:  1.20 (0.23), residues: 474
  sheet: -3.93 (1.72), residues: 10
  loop : -2.29 (0.36), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 222 
 HIS   0.003   0.001   HIS B 348 
 PHE   0.019   0.002   PHE B 236 
 TYR   0.020   0.002   TYR B 265 
 ARG   0.005   0.001   ARG A 272 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ILE cc_start: 0.8281 (mt) cc_final: 0.7959 (mt)
REVERT: B  222 TRP cc_start: 0.6801 (t-100) cc_final: 0.6394 (t-100)
REVERT: B  262 TYR cc_start: 0.7590 (m-80) cc_final: 0.7263 (m-80)
REVERT: B  314 MET cc_start: 0.7150 (mmm) cc_final: 0.6855 (mmm)
REVERT: B  436 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7634 (tmmt)
REVERT: C  440 ARG cc_start: 0.7742 (mmp80) cc_final: 0.7535 (mmm160)
REVERT: C  463 TYR cc_start: 0.6920 (t80) cc_final: 0.6488 (t80)
REVERT: C  493 ASN cc_start: 0.8205 (m-40) cc_final: 0.7996 (m-40)
  outliers start: 9
  outliers final: 6
  residues processed: 126
  average time/residue: 0.1668
  time to fit residues: 27.9769
Evaluate side-chains
  127 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain C residue  464 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0000
   chunk 41 optimal weight:    4.9990
   chunk 45 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 38 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.168010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.135043 restraints weight = 8851.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.138575 restraints weight = 5355.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.140864 restraints weight = 3889.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6051  Z= 0.173
  Angle     :  0.544   8.298   8303  Z= 0.277
  Chirality :  0.040   0.265    989
  Planarity :  0.003   0.040    949
  Dihedral  :  8.335  59.086   1477
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.18 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 (0.31), residues: 705
  helix:  1.58 (0.23), residues: 475
  sheet: -4.23 (1.51), residues: 10
  loop : -2.07 (0.37), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 327 
 HIS   0.002   0.001   HIS C 465 
 PHE   0.019   0.001   PHE A 236 
 TYR   0.015   0.001   TYR B 262 
 ARG   0.003   0.000   ARG A 432 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ILE cc_start: 0.8289 (mt) cc_final: 0.7999 (mt)
REVERT: A  404 LEU cc_start: 0.8080 (mm) cc_final: 0.7861 (mm)
REVERT: B  218 PHE cc_start: 0.8336 (t80) cc_final: 0.7281 (t80)
REVERT: B  222 TRP cc_start: 0.6668 (t-100) cc_final: 0.6272 (t-100)
REVERT: B  262 TYR cc_start: 0.7487 (m-80) cc_final: 0.7257 (m-80)
REVERT: B  298 LYS cc_start: 0.7707 (mttp) cc_final: 0.7314 (mttp)
REVERT: B  358 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7898 (mttp)
REVERT: B  436 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7742 (tmmt)
REVERT: C  463 TYR cc_start: 0.6954 (t80) cc_final: 0.6587 (t80)
  outliers start: 10
  outliers final: 7
  residues processed: 131
  average time/residue: 0.1810
  time to fit residues: 31.2511
Evaluate side-chains
  131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain C residue  464 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.166538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.132250 restraints weight = 8926.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.135861 restraints weight = 5276.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.138239 restraints weight = 3846.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6051  Z= 0.262
  Angle     :  0.575   8.042   8303  Z= 0.293
  Chirality :  0.042   0.260    989
  Planarity :  0.003   0.045    949
  Dihedral  :  8.313  59.125   1477
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.86 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.31), residues: 705
  helix:  1.56 (0.23), residues: 473
  sheet: -4.31 (1.49), residues: 10
  loop : -2.03 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 327 
 HIS   0.005   0.001   HIS B 348 
 PHE   0.019   0.002   PHE A 312 
 TYR   0.022   0.001   TYR B 265 
 ARG   0.002   0.000   ARG A 417 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6638 (mm)
REVERT: A  349 ILE cc_start: 0.8366 (mt) cc_final: 0.8079 (mt)
REVERT: A  404 LEU cc_start: 0.8056 (mm) cc_final: 0.7810 (mm)
REVERT: B  222 TRP cc_start: 0.6807 (t-100) cc_final: 0.6389 (t-100)
REVERT: B  298 LYS cc_start: 0.7770 (mttp) cc_final: 0.7420 (mttp)
REVERT: B  327 TRP cc_start: 0.7681 (t60) cc_final: 0.7475 (t60)
REVERT: B  358 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7935 (mttp)
REVERT: B  377 CYS cc_start: 0.4981 (m) cc_final: 0.4772 (m)
REVERT: C  463 TYR cc_start: 0.7160 (t80) cc_final: 0.6821 (t80)
  outliers start: 14
  outliers final: 7
  residues processed: 130
  average time/residue: 0.1783
  time to fit residues: 30.1137
Evaluate side-chains
  132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain C residue  464 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 58 optimal weight:    0.0980
   chunk 62 optimal weight:    0.3980
   chunk 68 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0870
   chunk 46 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0980
   chunk 26 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.2358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.170026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.135402 restraints weight = 8776.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.139214 restraints weight = 5085.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.141703 restraints weight = 3662.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6051  Z= 0.163
  Angle     :  0.523   7.853   8303  Z= 0.266
  Chirality :  0.039   0.245    989
  Planarity :  0.003   0.039    949
  Dihedral  :  7.953  58.911   1477
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.29 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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:  0.96 (0.32), residues: 705
  helix:  1.83 (0.23), residues: 473
  sheet: -4.30 (1.45), residues: 10
  loop : -1.84 (0.38), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 327 
 HIS   0.002   0.001   HIS B 348 
 PHE   0.016   0.001   PHE A 312 
 TYR   0.017   0.001   TYR B 262 
 ARG   0.003   0.000   ARG C 440 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6540 (mm)
REVERT: A  272 ARG cc_start: 0.7224 (tmm-80) cc_final: 0.6848 (tmt170)
REVERT: A  349 ILE cc_start: 0.8267 (mt) cc_final: 0.7950 (mt)
REVERT: A  404 LEU cc_start: 0.8042 (mm) cc_final: 0.7790 (mm)
REVERT: B  218 PHE cc_start: 0.8418 (t80) cc_final: 0.7627 (t80)
REVERT: B  222 TRP cc_start: 0.6629 (t-100) cc_final: 0.6185 (t-100)
REVERT: B  298 LYS cc_start: 0.7724 (mttp) cc_final: 0.7351 (mttp)
REVERT: B  358 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7445 (mttm)
REVERT: B  377 CYS cc_start: 0.5247 (m) cc_final: 0.4986 (m)
REVERT: C  463 TYR cc_start: 0.7296 (t80) cc_final: 0.6965 (t80)
  outliers start: 16
  outliers final: 9
  residues processed: 133
  average time/residue: 0.1760
  time to fit residues: 30.5093
Evaluate side-chains
  133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  461 ASN
Chi-restraints excluded: chain C residue  464 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    0.0570
   chunk 60 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 50 optimal weight:    0.4980
   chunk 51 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.168368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.133330 restraints weight = 8774.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.137086 restraints weight = 5128.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.139584 restraints weight = 3701.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6051  Z= 0.217
  Angle     :  0.555   8.158   8303  Z= 0.283
  Chirality :  0.041   0.244    989
  Planarity :  0.003   0.042    949
  Dihedral  :  7.980  58.767   1477
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.43 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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:  0.82 (0.31), residues: 705
  helix:  1.70 (0.23), residues: 473
  sheet: -4.28 (1.50), residues: 10
  loop : -1.85 (0.38), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 327 
 HIS   0.003   0.001   HIS B 348 
 PHE   0.018   0.001   PHE A 312 
 TYR   0.018   0.001   TYR B 265 
 ARG   0.003   0.000   ARG C 440 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6583 (mm)
REVERT: A  272 ARG cc_start: 0.7305 (tmm-80) cc_final: 0.6962 (tmt170)
REVERT: A  349 ILE cc_start: 0.8323 (mt) cc_final: 0.8008 (mt)
REVERT: A  404 LEU cc_start: 0.8032 (mm) cc_final: 0.7791 (mm)
REVERT: B  218 PHE cc_start: 0.8456 (t80) cc_final: 0.7547 (t80)
REVERT: B  222 TRP cc_start: 0.6704 (t-100) cc_final: 0.6268 (t-100)
REVERT: B  298 LYS cc_start: 0.7740 (mttp) cc_final: 0.7455 (mttp)
REVERT: B  358 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7807 (mttp)
REVERT: C  463 TYR cc_start: 0.7347 (t80) cc_final: 0.7053 (t80)
  outliers start: 14
  outliers final: 6
  residues processed: 128
  average time/residue: 0.1805
  time to fit residues: 30.1060
Evaluate side-chains
  129 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  461 ASN
Chi-restraints excluded: chain C residue  464 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.166178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.131304 restraints weight = 8888.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.135029 restraints weight = 5216.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.137463 restraints weight = 3775.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6051  Z= 0.294
  Angle     :  0.603   7.797   8303  Z= 0.308
  Chirality :  0.043   0.260    989
  Planarity :  0.003   0.047    949
  Dihedral  :  8.050  57.443   1477
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.96 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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:  0.56 (0.31), residues: 705
  helix:  1.49 (0.23), residues: 474
  sheet: -3.63 (0.94), residues: 20
  loop : -1.84 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 327 
 HIS   0.004   0.001   HIS B 348 
 PHE   0.020   0.002   PHE A 312 
 TYR   0.024   0.002   TYR B 265 
 ARG   0.003   0.000   ARG C 440 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6585 (mm)
REVERT: A  272 ARG cc_start: 0.7462 (tmm-80) cc_final: 0.6866 (tmt170)
REVERT: A  349 ILE cc_start: 0.8391 (mt) cc_final: 0.8084 (mt)
REVERT: A  404 LEU cc_start: 0.8037 (mm) cc_final: 0.7784 (mm)
REVERT: A  444 TYR cc_start: 0.8125 (t80) cc_final: 0.7535 (t80)
REVERT: B  327 TRP cc_start: 0.7632 (t60) cc_final: 0.7179 (t60)
REVERT: B  358 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7875 (mttp)
REVERT: B  486 LEU cc_start: 0.7984 (tp) cc_final: 0.7740 (tp)
  outliers start: 15
  outliers final: 8
  residues processed: 128
  average time/residue: 0.1727
  time to fit residues: 29.2904
Evaluate side-chains
  132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  504 TRP
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  461 ASN
Chi-restraints excluded: chain C residue  464 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 20 optimal weight:    0.0970
   chunk 10 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   overall best weight:    0.3978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.168703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.134329 restraints weight = 8776.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.137978 restraints weight = 5204.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.140365 restraints weight = 3794.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6051  Z= 0.195
  Angle     :  0.560   8.327   8303  Z= 0.286
  Chirality :  0.040   0.251    989
  Planarity :  0.003   0.042    949
  Dihedral  :  7.816  58.843   1477
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.68 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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:  0.79 (0.31), residues: 705
  helix:  1.67 (0.23), residues: 472
  sheet: -4.16 (1.54), residues: 10
  loop : -1.82 (0.37), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 327 
 HIS   0.003   0.001   HIS B 348 
 PHE   0.020   0.001   PHE B 236 
 TYR   0.025   0.001   TYR C 463 
 ARG   0.004   0.000   ARG C 440 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6603 (mm)
REVERT: A  272 ARG cc_start: 0.7411 (tmm-80) cc_final: 0.6895 (tmt170)
REVERT: A  349 ILE cc_start: 0.8319 (mt) cc_final: 0.8015 (mt)
REVERT: A  404 LEU cc_start: 0.8047 (mm) cc_final: 0.7794 (mm)
REVERT: B  222 TRP cc_start: 0.6705 (t-100) cc_final: 0.6371 (t-100)
REVERT: B  327 TRP cc_start: 0.7522 (t60) cc_final: 0.7223 (t60)
REVERT: B  358 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7860 (mttp)
REVERT: C  463 TYR cc_start: 0.6721 (t80) cc_final: 0.6340 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 129
  average time/residue: 0.1622
  time to fit residues: 27.8851
Evaluate side-chains
  132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  461 ASN
Chi-restraints excluded: chain C residue  464 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0870
   chunk 51 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 48 optimal weight:    0.1980
   chunk 28 optimal weight:    0.0870
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.170426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.137560 restraints weight = 8869.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.141050 restraints weight = 5270.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.143354 restraints weight = 3833.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6051  Z= 0.194
  Angle     :  0.564   9.179   8303  Z= 0.285
  Chirality :  0.040   0.242    989
  Planarity :  0.003   0.041    949
  Dihedral  :  7.766  59.784   1477
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.50 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 (0.31), residues: 705
  helix:  1.71 (0.23), residues: 473
  sheet: -4.07 (1.56), residues: 10
  loop : -1.81 (0.38), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 327 
 HIS   0.003   0.001   HIS B 348 
 PHE   0.018   0.001   PHE A 312 
 TYR   0.019   0.001   TYR C 463 
 ARG   0.004   0.000   ARG C 440 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6610 (mm)
REVERT: A  272 ARG cc_start: 0.7486 (tmm-80) cc_final: 0.7011 (tmt170)
REVERT: A  349 ILE cc_start: 0.8340 (mt) cc_final: 0.8068 (mt)
REVERT: A  404 LEU cc_start: 0.8068 (mm) cc_final: 0.7825 (mm)
REVERT: B  222 TRP cc_start: 0.6463 (t-100) cc_final: 0.6114 (t-100)
REVERT: B  327 TRP cc_start: 0.7502 (t60) cc_final: 0.7090 (t60)
REVERT: B  358 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7862 (mttp)
REVERT: C  440 ARG cc_start: 0.7459 (mmp80) cc_final: 0.7234 (mmm160)
REVERT: C  463 TYR cc_start: 0.6770 (t80) cc_final: 0.6423 (t80)
  outliers start: 12
  outliers final: 7
  residues processed: 125
  average time/residue: 0.1837
  time to fit residues: 29.9867
Evaluate side-chains
  130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  504 TRP
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain C residue  464 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.166022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.131591 restraints weight = 8902.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135198 restraints weight = 5293.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.137538 restraints weight = 3854.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6051  Z= 0.300
  Angle     :  0.641  11.561   8303  Z= 0.320
  Chirality :  0.043   0.258    989
  Planarity :  0.004   0.046    949
  Dihedral  :  7.901  59.132   1477
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.57 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 (0.31), residues: 705
  helix:  1.49 (0.23), residues: 474
  sheet: -4.04 (1.59), residues: 10
  loop : -1.84 (0.37), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 327 
 HIS   0.004   0.001   HIS B 348 
 PHE   0.029   0.002   PHE B 236 
 TYR   0.024   0.002   TYR B 265 
 ARG   0.003   0.000   ARG C 440 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6639 (mm)
REVERT: A  272 ARG cc_start: 0.7506 (tmm-80) cc_final: 0.6768 (tmt170)
REVERT: A  349 ILE cc_start: 0.8426 (mt) cc_final: 0.8129 (mt)
REVERT: A  404 LEU cc_start: 0.8071 (mm) cc_final: 0.7808 (mm)
REVERT: A  444 TYR cc_start: 0.8120 (t80) cc_final: 0.7562 (t80)
REVERT: B  222 TRP cc_start: 0.6600 (t-100) cc_final: 0.6194 (t-100)
REVERT: B  327 TRP cc_start: 0.7616 (t60) cc_final: 0.7169 (t60)
REVERT: B  358 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7549 (mtmm)
REVERT: C  463 TYR cc_start: 0.6803 (t80) cc_final: 0.6434 (t80)
  outliers start: 9
  outliers final: 6
  residues processed: 128
  average time/residue: 0.1634
  time to fit residues: 27.8261
Evaluate side-chains
  132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  504 TRP
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain C residue  464 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.166246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.131684 restraints weight = 8856.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.135268 restraints weight = 5260.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.137611 restraints weight = 3845.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6051  Z= 0.290
  Angle     :  0.636  12.875   8303  Z= 0.318
  Chirality :  0.042   0.259    989
  Planarity :  0.004   0.049    949
  Dihedral  :  7.854  59.220   1477
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.57 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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:  0.52 (0.31), residues: 705
  helix:  1.44 (0.23), residues: 474
  sheet: -3.57 (0.96), residues: 20
  loop : -1.81 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP B 327 
 HIS   0.004   0.001   HIS B 348 
 PHE   0.030   0.002   PHE B 236 
 TYR   0.023   0.002   TYR B 265 
 ARG   0.004   0.000   ARG B 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1988.92 seconds
wall clock time: 36 minutes 20.53 seconds (2180.53 seconds total)