Starting phenix.real_space_refine
on Tue Mar 11 16:41:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ddo_30655/03_2025/7ddo_30655.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ddo_30655/03_2025/7ddo_30655.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ddo_30655/03_2025/7ddo_30655.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ddo_30655/03_2025/7ddo_30655.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ddo_30655/03_2025/7ddo_30655.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ddo_30655/03_2025/7ddo_30655.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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
     Zn      1      6.06       5
     S      37      5.16       5
     C    4133      2.51       5
     N    1067      2.21       5
     O    1230      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6468
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "C"
      Number of atoms: 1534
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1534
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.61, per 1000 atoms: 1.02
  Number of scatterers: 6468
  At special positions: 0
  Unit cell: (101.362, 96.3937, 106.331, 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)
     Zn      1     29.99
     S      37     16.00
     O    1230      8.00
     N    1067      7.00
     C    4133      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG A 902 " - " ASN A 546 "
      " NAG A 903 " - " ASN A  90 "
      " NAG A 904 " - " ASN A  53 "
      " NAG C 601 " - " ASN C 343 "
  Time building additional restraints: 1.66
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "


  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      55.6% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.599A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.737A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.621A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.564A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU A 108 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 103 through 108'
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 143 through 155
      removed outlier: 4.233A  pdb=" N   ASN A 149 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 4.192A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 252
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.720A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.643A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.591A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.565A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.666A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 485
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.619A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.780A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.929A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 502 through 506
      removed outlier: 3.715A  pdb=" N   GLN C 506 " --> pdb=" O   VAL C 503 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.815A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.174A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.774A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE C 358 " --> pdb=" O   VAL C 395 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   VAL C 433 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LYS C 378 " --> pdb=" O   VAL C 433 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 452 through 453
    Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 474
      removed outlier: 3.815A  pdb=" N   TYR C 489 " --> pdb=" O   TYR C 473 " (cutoff:3.500A)

    304 hydrogen bonds defined for protein.
    875 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: 1.67

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2077
        1.34 -     1.46: 1660
        1.46 -     1.58: 2854
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6649
  Sorted by residual:
  bond pdb=" C1  NAG A 902 "
       pdb=" O5  NAG A 902 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.27e+00
  bond pdb=" C1  NAG A 903 "
       pdb=" O5  NAG A 903 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C1  NAG A 904 "
       pdb=" O5  NAG A 904 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.99e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  bond pdb=" CA  VAL C 524 "
       pdb=" CB  VAL C 524 "
    ideal  model  delta    sigma   weight residual
    1.531  1.545 -0.014 1.11e-02 8.12e+03 1.61e+00
  ... (remaining 6644 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 8752
        1.37 -     2.74: 223
        2.74 -     4.11: 55
        4.11 -     5.48: 9
        5.48 -     6.85: 3
  Bond angle restraints: 9042
  Sorted by residual:
  angle pdb=" N   VAL C 524 "
        pdb=" CA  VAL C 524 "
        pdb=" C   VAL C 524 "
      ideal   model   delta    sigma   weight residual
     106.53  110.71   -4.18 1.41e+00 5.03e-01 8.81e+00
  angle pdb=" N   ILE A 544 "
        pdb=" CA  ILE A 544 "
        pdb=" C   ILE A 544 "
      ideal   model   delta    sigma   weight residual
     113.22  109.75    3.47 1.23e+00 6.61e-01 7.95e+00
  angle pdb=" N   GLU A 589 "
        pdb=" CA  GLU A 589 "
        pdb=" C   GLU A 589 "
      ideal   model   delta    sigma   weight residual
     109.81  115.20   -5.39 2.21e+00 2.05e-01 5.95e+00
  angle pdb=" C   LEU A 144 "
        pdb=" N   GLU A 145 "
        pdb=" CA  GLU A 145 "
      ideal   model   delta    sigma   weight residual
     120.97  124.12   -3.15 1.48e+00 4.57e-01 4.53e+00
  angle pdb=" N   VAL A 506 "
        pdb=" CA  VAL A 506 "
        pdb=" C   VAL A 506 "
      ideal   model   delta    sigma   weight residual
     111.45  109.52    1.93 9.30e-01 1.16e+00 4.30e+00
  ... (remaining 9037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 3558
       17.31 -    34.63: 319
       34.63 -    51.94: 68
       51.94 -    69.25: 15
       69.25 -    86.56: 12
  Dihedral angle restraints: 3972
    sinusoidal: 1648
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    6.44   86.56     1      1.00e+01 1.00e-02 9.02e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   25.85   67.15     1      1.00e+01 1.00e-02 5.87e+01
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -22.59  -63.41     1      1.00e+01 1.00e-02 5.30e+01
  ... (remaining 3969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 571
       0.028 -    0.056: 251
       0.056 -    0.084: 80
       0.084 -    0.111: 51
       0.111 -    0.139: 6
  Chirality restraints: 959
  Sorted by residual:
  chirality pdb=" CA  GLU A 589 "
            pdb=" N   GLU A 589 "
            pdb=" C   GLU A 589 "
            pdb=" CB  GLU A 589 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.85e-01
  chirality pdb=" CA  ILE C 434 "
            pdb=" N   ILE C 434 "
            pdb=" C   ILE C 434 "
            pdb=" CB  ILE C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.71e-01
  chirality pdb=" CA  THR C 372 "
            pdb=" N   THR C 372 "
            pdb=" C   THR C 372 "
            pdb=" CB  THR C 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.12 2.00e-01 2.50e+01 3.69e-01
  ... (remaining 956 not shown)

  Planarity restraints: 1173
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "    0.025 5.00e-02 4.00e+02   3.80e-02 2.31e+00
        pdb=" N   PRO A 583 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 234 "    0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO A 235 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 235 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 235 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 462 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO C 463 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C 463 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 463 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1170 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 79
        2.63 -     3.20: 5772
        3.20 -     3.76: 10356
        3.76 -     4.33: 14430
        4.33 -     4.90: 23518
  Nonbonded interactions: 54155
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 901 "
     model   vdw
     2.062 2.230
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" O   VAL A 485 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD2 ASP A 509 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   LEU A 278 "
            pdb=" OG1 THR A 282 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE1 GLU C 406 "
            pdb=" OH  TYR C 495 "
     model   vdw
     2.260 3.040
  ... (remaining 54150 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.790
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6649  Z= 0.174
  Angle     :  0.549   6.846   9042  Z= 0.311
  Chirality :  0.039   0.139    959
  Planarity :  0.003   0.038   1169
  Dihedral  : 14.130  86.321   2461
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  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: -1.39 (0.27), residues: 788
  helix: -0.30 (0.23), residues: 403
  sheet: -1.61 (0.64), residues: 57
  loop : -1.49 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.014   0.001   PHE C 490 
 TYR   0.014   0.001   TYR A 381 
 ARG   0.002   0.000   ARG A 219 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A  190 MET cc_start: 0.8484 (tmm) cc_final: 0.8223 (tmm)
REVERT: A  360 MET cc_start: 0.8388 (ttt) cc_final: 0.8176 (ptm)
REVERT: A  382 ASP cc_start: 0.8526 (m-30) cc_final: 0.8112 (m-30)
REVERT: C  396 TYR cc_start: 0.6757 (m-80) cc_final: 0.6205 (m-80)
REVERT: C  408 ARG cc_start: 0.8277 (ptp90) cc_final: 0.7999 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1810
  time to fit residues: 34.3123
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 59 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 70 optimal weight:    6.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A  58 ASN
A 210 ASN
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 ASN
A 338 ASN
C 460 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.143957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.114025 restraints weight = 18986.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 3.55
r_work: 0.3016 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6649  Z= 0.295
  Angle     :  0.591   6.939   9042  Z= 0.302
  Chirality :  0.044   0.148    959
  Planarity :  0.004   0.039   1169
  Dihedral  :  5.069  44.198    945
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.48 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.28), residues: 788
  helix:  0.46 (0.25), residues: 405
  sheet: -1.08 (0.65), residues: 57
  loop : -1.04 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 477 
 HIS   0.005   0.001   HIS A  34 
 PHE   0.018   0.002   PHE C 490 
 TYR   0.030   0.002   TYR A 381 
 ARG   0.003   0.001   ARG A 219 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A  382 ASP cc_start: 0.8660 (m-30) cc_final: 0.8267 (m-30)
REVERT: A  489 GLU cc_start: 0.8695 (pm20) cc_final: 0.8162 (pm20)
REVERT: C  356 LYS cc_start: 0.8093 (mppt) cc_final: 0.7707 (mmtp)
REVERT: C  408 ARG cc_start: 0.8496 (ptp90) cc_final: 0.8201 (ptp-170)
  outliers start: 10
  outliers final: 9
  residues processed: 117
  average time/residue: 0.1522
  time to fit residues: 25.1796
Evaluate side-chains
  111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  514 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 62 optimal weight:   20.0000
   chunk 52 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** 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 = 0.3712 r_free = 0.3712 target = 0.146775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.116487 restraints weight = 14067.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.45
r_work: 0.3125 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6649  Z= 0.179
  Angle     :  0.523   6.306   9042  Z= 0.266
  Chirality :  0.041   0.147    959
  Planarity :  0.004   0.036   1169
  Dihedral  :  4.684  43.878    945
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.92 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.29), residues: 788
  helix:  0.97 (0.25), residues: 409
  sheet: -1.01 (0.64), residues: 57
  loop : -0.79 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 345 
 PHE   0.016   0.001   PHE C 490 
 TYR   0.017   0.001   TYR A 183 
 ARG   0.003   0.000   ARG A 219 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A  270 MET cc_start: 0.8558 (tpt) cc_final: 0.7814 (tpt)
REVERT: A  382 ASP cc_start: 0.8592 (m-30) cc_final: 0.8168 (m-30)
REVERT: A  474 MET cc_start: 0.8555 (mmp) cc_final: 0.8201 (mmp)
REVERT: A  489 GLU cc_start: 0.8685 (pm20) cc_final: 0.8098 (pm20)
REVERT: C  356 LYS cc_start: 0.8045 (mppt) cc_final: 0.7798 (mmtt)
REVERT: C  396 TYR cc_start: 0.6977 (m-80) cc_final: 0.6388 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 119
  average time/residue: 0.1463
  time to fit residues: 25.0200
Evaluate side-chains
  102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  514 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:   30.0000
   chunk 23 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0070
   chunk 26 optimal weight:    0.0770
   chunk 62 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    1.5560

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.145376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.112272 restraints weight = 12298.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.70
r_work: 0.3090 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6649  Z= 0.207
  Angle     :  0.537   7.278   9042  Z= 0.272
  Chirality :  0.042   0.145    959
  Planarity :  0.004   0.037   1169
  Dihedral  :  4.639  41.689    945
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.93 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.29), residues: 788
  helix:  1.07 (0.25), residues: 409
  sheet: -0.88 (0.65), residues: 57
  loop : -0.68 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 345 
 PHE   0.011   0.001   PHE C 490 
 TYR   0.018   0.001   TYR A 381 
 ARG   0.003   0.000   ARG A 219 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A  350 ASP cc_start: 0.7958 (t0) cc_final: 0.7223 (p0)
REVERT: A  360 MET cc_start: 0.8395 (ttt) cc_final: 0.8174 (ptm)
REVERT: A  382 ASP cc_start: 0.8618 (m-30) cc_final: 0.8024 (m-30)
REVERT: A  474 MET cc_start: 0.8500 (mmp) cc_final: 0.8109 (mmp)
REVERT: A  489 GLU cc_start: 0.8685 (pm20) cc_final: 0.8021 (pm20)
REVERT: A  589 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8245 (tm-30)
REVERT: C  343 ASN cc_start: 0.7427 (m-40) cc_final: 0.6827 (p0)
REVERT: C  356 LYS cc_start: 0.8090 (mppt) cc_final: 0.7789 (mmtp)
REVERT: C  396 TYR cc_start: 0.6905 (m-80) cc_final: 0.6242 (m-80)
REVERT: C  489 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.5560 (p90)
  outliers start: 9
  outliers final: 8
  residues processed: 109
  average time/residue: 0.1511
  time to fit residues: 23.4050
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  514 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0980
   chunk 39 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 58 optimal weight:    0.1980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.149636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.119161 restraints weight = 17359.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 3.09
r_work: 0.3113 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6649  Z= 0.133
  Angle     :  0.489   6.712   9042  Z= 0.249
  Chirality :  0.040   0.146    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.221  36.765    945
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.36 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.30), residues: 788
  helix:  1.42 (0.26), residues: 404
  sheet: -0.57 (0.67), residues: 55
  loop : -0.45 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.008   0.001   PHE C 490 
 TYR   0.016   0.001   TYR A 183 
 ARG   0.003   0.000   ARG A 219 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  267 LEU cc_start: 0.8385 (mt) cc_final: 0.8152 (mt)
REVERT: A  270 MET cc_start: 0.8410 (tpt) cc_final: 0.8127 (tpt)
REVERT: A  350 ASP cc_start: 0.7945 (t0) cc_final: 0.7231 (p0)
REVERT: A  382 ASP cc_start: 0.8543 (m-30) cc_final: 0.8146 (m-30)
REVERT: A  474 MET cc_start: 0.8541 (mmp) cc_final: 0.8197 (mmp)
REVERT: A  489 GLU cc_start: 0.8713 (pm20) cc_final: 0.8080 (pm20)
REVERT: C  343 ASN cc_start: 0.7071 (m-40) cc_final: 0.6589 (p0)
REVERT: C  489 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.5895 (p90)
  outliers start: 10
  outliers final: 6
  residues processed: 121
  average time/residue: 0.1456
  time to fit residues: 24.9865
Evaluate side-chains
  111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  514 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 46 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 58 optimal weight:    0.1980
   chunk 72 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.149916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118656 restraints weight = 18668.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 3.37
r_work: 0.3104 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6649  Z= 0.144
  Angle     :  0.503   6.923   9042  Z= 0.257
  Chirality :  0.040   0.153    959
  Planarity :  0.004   0.030   1169
  Dihedral  :  4.093  34.238    945
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.79 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.30), residues: 788
  helix:  1.47 (0.26), residues: 404
  sheet: -0.49 (0.68), residues: 55
  loop : -0.25 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.014   0.001   PHE C 490 
 TYR   0.015   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 219 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A  249 MET cc_start: 0.8388 (ptp) cc_final: 0.7977 (ttp)
REVERT: A  267 LEU cc_start: 0.8541 (mt) cc_final: 0.8227 (mt)
REVERT: A  270 MET cc_start: 0.8486 (tpt) cc_final: 0.8086 (tpt)
REVERT: A  350 ASP cc_start: 0.8037 (t0) cc_final: 0.7380 (p0)
REVERT: A  360 MET cc_start: 0.7885 (ptm) cc_final: 0.7524 (ptm)
REVERT: A  474 MET cc_start: 0.8534 (mmp) cc_final: 0.8162 (mmp)
REVERT: A  489 GLU cc_start: 0.8676 (pm20) cc_final: 0.8046 (pm20)
REVERT: C  343 ASN cc_start: 0.6970 (m-40) cc_final: 0.6616 (p0)
REVERT: C  489 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6036 (p90)
  outliers start: 11
  outliers final: 5
  residues processed: 111
  average time/residue: 0.1528
  time to fit residues: 24.4031
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 64 optimal weight:   20.0000
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN
A 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.144357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.113083 restraints weight = 18990.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 3.40
r_work: 0.2995 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6649  Z= 0.262
  Angle     :  0.580  11.044   9042  Z= 0.294
  Chirality :  0.043   0.159    959
  Planarity :  0.004   0.033   1169
  Dihedral  :  4.460  31.506    945
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.51 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.30), residues: 788
  helix:  1.10 (0.25), residues: 411
  sheet: -0.38 (0.69), residues: 55
  loop : -0.28 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 594 
 HIS   0.006   0.001   HIS A  34 
 PHE   0.010   0.002   PHE A 274 
 TYR   0.020   0.002   TYR A 381 
 ARG   0.004   0.001   ARG A 559 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A   82 MET cc_start: 0.8148 (mtp) cc_final: 0.7774 (mpp)
REVERT: A  350 ASP cc_start: 0.8156 (t0) cc_final: 0.7348 (p0)
REVERT: A  382 ASP cc_start: 0.8483 (m-30) cc_final: 0.8023 (m-30)
REVERT: A  401 HIS cc_start: 0.9036 (OUTLIER) cc_final: 0.8457 (m-70)
REVERT: C  396 TYR cc_start: 0.6885 (m-80) cc_final: 0.6176 (m-80)
REVERT: C  489 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.5487 (p90)
  outliers start: 15
  outliers final: 8
  residues processed: 113
  average time/residue: 0.1496
  time to fit residues: 24.3263
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:   20.0000
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 39 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN
A 345 HIS
C 354 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.147128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.116102 restraints weight = 18663.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 3.41
r_work: 0.3046 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6649  Z= 0.175
  Angle     :  0.561  13.011   9042  Z= 0.281
  Chirality :  0.042   0.145    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.449  35.972    945
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 15.23 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.30), residues: 788
  helix:  1.30 (0.26), residues: 407
  sheet: -0.49 (0.66), residues: 55
  loop : -0.07 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.036   0.001   PHE A 603 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 514 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A   82 MET cc_start: 0.8133 (mtp) cc_final: 0.7757 (mpp)
REVERT: A  249 MET cc_start: 0.8471 (ptp) cc_final: 0.8062 (ttp)
REVERT: A  267 LEU cc_start: 0.8486 (mt) cc_final: 0.8196 (mt)
REVERT: A  270 MET cc_start: 0.8499 (tpt) cc_final: 0.8079 (tpt)
REVERT: A  350 ASP cc_start: 0.8153 (t0) cc_final: 0.7366 (p0)
REVERT: A  382 ASP cc_start: 0.8441 (m-30) cc_final: 0.7987 (m-30)
REVERT: A  474 MET cc_start: 0.8595 (mmp) cc_final: 0.8322 (mmp)
REVERT: A  489 GLU cc_start: 0.8683 (pm20) cc_final: 0.8199 (pm20)
REVERT: A  589 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8289 (tm-30)
REVERT: C  396 TYR cc_start: 0.6890 (m-80) cc_final: 0.6263 (m-80)
REVERT: C  489 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6035 (p90)
  outliers start: 9
  outliers final: 7
  residues processed: 102
  average time/residue: 0.1481
  time to fit residues: 21.7234
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 77 optimal weight:   20.0000
   chunk 28 optimal weight:    4.9990
   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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
A 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.145993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.114282 restraints weight = 13718.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.93
r_work: 0.3114 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   6649  Z= 0.222
  Angle     :  0.562  11.670   9042  Z= 0.284
  Chirality :  0.043   0.144    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.507  34.238    945
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.37 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.30), residues: 788
  helix:  1.22 (0.25), residues: 407
  sheet: -0.18 (0.69), residues: 50
  loop : -0.19 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.030   0.001   PHE A 603 
 TYR   0.017   0.001   TYR A 183 
 ARG   0.003   0.000   ARG A 559 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A   82 MET cc_start: 0.8053 (mtp) cc_final: 0.7731 (mpp)
REVERT: A  267 LEU cc_start: 0.8412 (mt) cc_final: 0.8083 (mt)
REVERT: A  270 MET cc_start: 0.8535 (tpt) cc_final: 0.8023 (tpt)
REVERT: A  350 ASP cc_start: 0.8069 (t0) cc_final: 0.7251 (p0)
REVERT: A  382 ASP cc_start: 0.8450 (m-30) cc_final: 0.7963 (m-30)
REVERT: A  474 MET cc_start: 0.8543 (mmp) cc_final: 0.8227 (mmp)
REVERT: C  396 TYR cc_start: 0.6888 (m-80) cc_final: 0.6188 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1482
  time to fit residues: 22.4176
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 76 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0060
   chunk 54 optimal weight:    0.7980
   chunk 65 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
A 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.148799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.117684 restraints weight = 19038.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 3.57
r_work: 0.3078 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   6649  Z= 0.157
  Angle     :  0.547  12.907   9042  Z= 0.272
  Chirality :  0.041   0.145    959
  Planarity :  0.004   0.032   1169
  Dihedral  :  4.373  35.843    945
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.51 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.30), residues: 788
  helix:  1.34 (0.26), residues: 409
  sheet: -0.23 (0.67), residues: 50
  loop : -0.14 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.029   0.001   PHE A 603 
 TYR   0.015   0.001   TYR A 183 
 ARG   0.003   0.000   ARG A 219 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A   82 MET cc_start: 0.8065 (mtp) cc_final: 0.7714 (mpp)
REVERT: A  249 MET cc_start: 0.8490 (ptp) cc_final: 0.8107 (ttp)
REVERT: A  267 LEU cc_start: 0.8527 (mt) cc_final: 0.8236 (mt)
REVERT: A  270 MET cc_start: 0.8511 (tpt) cc_final: 0.8041 (tpt)
REVERT: A  350 ASP cc_start: 0.8111 (t0) cc_final: 0.7388 (p0)
REVERT: A  382 ASP cc_start: 0.8405 (m-30) cc_final: 0.7959 (m-30)
REVERT: A  474 MET cc_start: 0.8605 (mmp) cc_final: 0.8323 (mmp)
REVERT: A  489 GLU cc_start: 0.8701 (pm20) cc_final: 0.8237 (pm20)
REVERT: C  396 TYR cc_start: 0.6939 (m-80) cc_final: 0.6230 (m-80)
REVERT: C  489 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.5859 (p90)
  outliers start: 11
  outliers final: 9
  residues processed: 107
  average time/residue: 0.1470
  time to fit residues: 22.7689
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 8 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 58 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
A 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.147820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.114092 restraints weight = 14543.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.96
r_work: 0.3154 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6649  Z= 0.181
  Angle     :  0.557  13.654   9042  Z= 0.280
  Chirality :  0.042   0.144    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.354  34.626    945
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 15.09 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.30), residues: 788
  helix:  1.30 (0.26), residues: 409
  sheet: -0.23 (0.67), residues: 50
  loop : -0.05 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 594 
 HIS   0.008   0.001   HIS A 345 
 PHE   0.029   0.001   PHE A 603 
 TYR   0.014   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 559 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3588.30 seconds
wall clock time: 62 minutes 20.28 seconds (3740.28 seconds total)