Starting phenix.real_space_refine
on Tue Feb 11 17:12:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ddo_30655/02_2025/7ddo_30655.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ddo_30655/02_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_30655/02_2025/7ddo_30655.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ddo_30655/02_2025/7ddo_30655.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ddo_30655/02_2025/7ddo_30655.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ddo_30655/02_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-5592/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: 6.14, per 1000 atoms: 0.95
  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 1.6 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: 0.59
  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: 1.73

  Time building geometry restraints manager: 1.88 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:             0.270
  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:                    0.050
  Process input model:                     22.270
  Find NCS groups from input model:        0.070
  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:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.590
-------------------------------------------------------------------------------
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  : 0.738 
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: 0.1800
  time to fit residues: 34.1698
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  : 0.705 
-------------------------------------------------------------------------------
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: 0.3020 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    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 = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
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  : 0.741 
Fit side-chains
REVERT: A  382 ASP cc_start: 0.8662 (m-30) cc_final: 0.8268 (m-30)
REVERT: A  489 GLU cc_start: 0.8688 (pm20) cc_final: 0.8147 (pm20)
REVERT: C  356 LYS cc_start: 0.8099 (mppt) cc_final: 0.7708 (mmtp)
REVERT: C  408 ARG cc_start: 0.8513 (ptp90) cc_final: 0.8222 (ptp-170)
  outliers start: 10
  outliers final: 9
  residues processed: 117
  average time/residue: 0.1675
  time to fit residues: 27.7388
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  : 0.747 
-------------------------------------------------------------------------------
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:    0.5980
   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:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3723 r_free = 0.3723 target = 0.147632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.117294 restraints weight = 14052.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.63
r_work: 0.3097 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6649  Z= 0.153
  Angle     :  0.510   6.405   9042  Z= 0.260
  Chirality :  0.041   0.147    959
  Planarity :  0.004   0.034   1169
  Dihedral  :  4.614  43.515    945
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 10.78 %
    Favored  : 87.50 %
  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:  0.25 (0.29), residues: 788
  helix:  1.06 (0.25), residues: 408
  sheet: -0.89 (0.65), residues: 55
  loop : -0.72 (0.34), residues: 325

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   0.014   0.001   PHE C 490 
 TYR   0.016   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
  129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A  270 MET cc_start: 0.8531 (tpt) cc_final: 0.7801 (tpt)
REVERT: A  382 ASP cc_start: 0.8566 (m-30) cc_final: 0.8162 (m-30)
REVERT: A  455 MET cc_start: 0.8735 (tmm) cc_final: 0.8036 (tmm)
REVERT: A  474 MET cc_start: 0.8533 (mmp) cc_final: 0.8208 (mmp)
REVERT: A  489 GLU cc_start: 0.8707 (pm20) cc_final: 0.8093 (pm20)
REVERT: C  356 LYS cc_start: 0.8053 (mppt) cc_final: 0.7797 (mmtt)
REVERT: C  396 TYR cc_start: 0.6974 (m-80) cc_final: 0.6385 (m-80)
REVERT: C  489 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.5828 (p90)
  outliers start: 12
  outliers final: 6
  residues processed: 123
  average time/residue: 0.1400
  time to fit residues: 24.8257
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
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:   20.0000
   chunk 23 optimal weight:    0.0010
   chunk 54 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0970
   chunk 62 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 32 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN
A 338 ASN
A 345 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.149876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.116735 restraints weight = 12265.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.73
r_work: 0.3165 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6649  Z= 0.131
  Angle     :  0.499   6.449   9042  Z= 0.252
  Chirality :  0.040   0.145    959
  Planarity :  0.004   0.033   1169
  Dihedral  :  4.323  42.739    945
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.07 %
    Favored  : 86.64 %
  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:  1.37 (0.26), residues: 404
  sheet: -0.84 (0.64), residues: 55
  loop : -0.56 (0.34), residues: 329

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   0.008   0.001   PHE A 230 
 TYR   0.016   0.001   TYR A 183 
 ARG   0.004   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
  118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  267 LEU cc_start: 0.8381 (mt) cc_final: 0.8162 (mt)
REVERT: A  350 ASP cc_start: 0.7912 (t0) cc_final: 0.7162 (p0)
REVERT: A  360 MET cc_start: 0.8086 (ptm) cc_final: 0.7832 (ptm)
REVERT: A  382 ASP cc_start: 0.8510 (m-30) cc_final: 0.8092 (m-30)
REVERT: A  474 MET cc_start: 0.8467 (mmp) cc_final: 0.8088 (mmp)
REVERT: A  489 GLU cc_start: 0.8700 (pm20) cc_final: 0.8048 (pm20)
REVERT: A  589 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8126 (tm-30)
REVERT: C  396 TYR cc_start: 0.6968 (m-80) cc_final: 0.6230 (m-80)
REVERT: C  474 GLN cc_start: 0.7597 (tt0) cc_final: 0.7334 (tt0)
REVERT: C  489 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.5886 (p90)
  outliers start: 9
  outliers final: 5
  residues processed: 114
  average time/residue: 0.1665
  time to fit residues: 26.6032
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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  514 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.147167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.116411 restraints weight = 17339.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 3.19
r_work: 0.3059 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6649  Z= 0.188
  Angle     :  0.525   9.435   9042  Z= 0.265
  Chirality :  0.041   0.140    959
  Planarity :  0.004   0.032   1169
  Dihedral  :  4.294  34.565    945
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.07 %
    Favored  : 86.49 %
  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:  0.65 (0.30), residues: 788
  helix:  1.26 (0.25), residues: 408
  sheet: -0.56 (0.67), residues: 55
  loop : -0.38 (0.34), residues: 325

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   0.011   0.001   PHE C 490 
 TYR   0.017   0.001   TYR A 381 
 ARG   0.002   0.000   ARG A 518 

*********************** 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
  115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A  267 LEU cc_start: 0.8400 (mt) cc_final: 0.8080 (mt)
REVERT: A  270 MET cc_start: 0.8553 (tpt) cc_final: 0.8078 (tpt)
REVERT: A  350 ASP cc_start: 0.8024 (t0) cc_final: 0.7380 (p0)
REVERT: A  360 MET cc_start: 0.8026 (ptm) cc_final: 0.7646 (ptm)
REVERT: A  474 MET cc_start: 0.8543 (mmp) cc_final: 0.8166 (mmp)
REVERT: A  489 GLU cc_start: 0.8684 (pm20) cc_final: 0.8041 (pm20)
REVERT: C  343 ASN cc_start: 0.7272 (m-40) cc_final: 0.6729 (p0)
REVERT: C  474 GLN cc_start: 0.7576 (tt0) cc_final: 0.7316 (tt0)
REVERT: C  489 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.5652 (p90)
REVERT: C  493 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6359 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1388
  time to fit residues: 22.5954
Evaluate side-chains
  107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 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
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:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 73 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.148431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.117761 restraints weight = 18642.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 3.43
r_work: 0.3082 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6649  Z= 0.162
  Angle     :  0.515   6.920   9042  Z= 0.262
  Chirality :  0.041   0.136    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.221  32.791    945
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.22 %
    Favored  : 85.34 %
  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:  0.79 (0.30), residues: 788
  helix:  1.39 (0.26), residues: 402
  sheet: -0.45 (0.69), residues: 55
  loop : -0.29 (0.35), residues: 331

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   0.015   0.001   PHE C 490 
 TYR   0.016   0.001   TYR A 183 
 ARG   0.003   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
  112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A   82 MET cc_start: 0.8043 (mtp) cc_final: 0.7704 (mpp)
REVERT: A  249 MET cc_start: 0.8420 (ptp) cc_final: 0.7998 (ttp)
REVERT: A  267 LEU cc_start: 0.8455 (mt) cc_final: 0.8195 (mt)
REVERT: A  270 MET cc_start: 0.8516 (tpt) cc_final: 0.8070 (tpt)
REVERT: A  350 ASP cc_start: 0.8097 (t0) cc_final: 0.7370 (p0)
REVERT: A  360 MET cc_start: 0.7948 (ptm) cc_final: 0.7610 (ptm)
REVERT: A  474 MET cc_start: 0.8558 (mmp) cc_final: 0.8198 (mmp)
REVERT: A  489 GLU cc_start: 0.8689 (pm20) cc_final: 0.8032 (pm20)
REVERT: C  396 TYR cc_start: 0.6949 (m-80) cc_final: 0.6215 (m-80)
REVERT: C  406 GLU cc_start: 0.8387 (tt0) cc_final: 0.8168 (tt0)
REVERT: C  474 GLN cc_start: 0.7546 (tt0) cc_final: 0.7284 (tt0)
REVERT: C  489 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6041 (p90)
REVERT: C  493 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6348 (tm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 108
  average time/residue: 0.1467
  time to fit residues: 23.0190
Evaluate side-chains
  102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0070
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 72 optimal weight:    8.9990
   chunk 64 optimal weight:   30.0000
   overall best weight:    0.6400

-------------------------------------------------------------------------------
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 = 0.3748 r_free = 0.3748 target = 0.150014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.119409 restraints weight = 18997.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 3.47
r_work: 0.3120 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    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 = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6649  Z= 0.141
  Angle     :  0.504   7.143   9042  Z= 0.256
  Chirality :  0.041   0.159    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.250  40.578    945
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.36 %
    Favored  : 85.06 %
  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:  0.92 (0.30), residues: 788
  helix:  1.46 (0.26), residues: 404
  sheet: -0.44 (0.68), residues: 55
  loop : -0.19 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.010   0.001   PHE C 490 
 TYR   0.010   0.001   TYR A 237 
 ARG   0.002   0.000   ARG A 219 

*********************** 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
  116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7905 (mtp) cc_final: 0.7614 (mpp)
REVERT: A  249 MET cc_start: 0.8406 (ptp) cc_final: 0.8016 (ttp)
REVERT: A  267 LEU cc_start: 0.8472 (mt) cc_final: 0.8177 (mt)
REVERT: A  270 MET cc_start: 0.8514 (tpt) cc_final: 0.8029 (tpt)
REVERT: A  350 ASP cc_start: 0.8019 (t0) cc_final: 0.7317 (p0)
REVERT: A  360 MET cc_start: 0.7873 (ptm) cc_final: 0.7583 (ptm)
REVERT: A  474 MET cc_start: 0.8561 (mmp) cc_final: 0.8202 (mmp)
REVERT: A  489 GLU cc_start: 0.8671 (pm20) cc_final: 0.8012 (pm20)
REVERT: C  396 TYR cc_start: 0.6945 (m-80) cc_final: 0.6258 (m-80)
REVERT: C  406 GLU cc_start: 0.8366 (tt0) cc_final: 0.8137 (tt0)
REVERT: C  489 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.5858 (p90)
REVERT: C  493 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6416 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 112
  average time/residue: 0.1555
  time to fit residues: 24.4323
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  189 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 77 optimal weight:   20.0000
   chunk 7 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 23 optimal weight:    0.1980
   chunk 39 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.147356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.117163 restraints weight = 18693.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 3.16
r_work: 0.3117 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6649  Z= 0.194
  Angle     :  0.531   7.261   9042  Z= 0.270
  Chirality :  0.042   0.156    959
  Planarity :  0.004   0.032   1169
  Dihedral  :  4.337  34.606    945
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.65 %
    Favored  : 84.91 %
  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:  0.85 (0.30), residues: 788
  helix:  1.39 (0.26), residues: 402
  sheet: -0.14 (0.71), residues: 50
  loop : -0.25 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 345 
 PHE   0.011   0.001   PHE C 490 
 TYR   0.016   0.001   TYR A 279 
 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
  111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7934 (mtp) cc_final: 0.7655 (mpp)
REVERT: A  249 MET cc_start: 0.8430 (ptp) cc_final: 0.8027 (ttp)
REVERT: A  267 LEU cc_start: 0.8553 (mt) cc_final: 0.8270 (mt)
REVERT: A  350 ASP cc_start: 0.8105 (t0) cc_final: 0.7375 (p0)
REVERT: A  360 MET cc_start: 0.7980 (ptm) cc_final: 0.7580 (ptm)
REVERT: C  396 TYR cc_start: 0.6956 (m-80) cc_final: 0.6344 (m-80)
REVERT: C  406 GLU cc_start: 0.8311 (tt0) cc_final: 0.8074 (tt0)
REVERT: C  489 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.5643 (p90)
REVERT: C  493 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.6485 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 106
  average time/residue: 0.1532
  time to fit residues: 22.9270
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
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  189 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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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
C 354 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.148496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.115008 restraints weight = 13748.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.88
r_work: 0.3171 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1981

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= 0.159
  Angle     :  0.519   7.429   9042  Z= 0.264
  Chirality :  0.041   0.148    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.277  34.779    945
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.22 %
    Favored  : 85.20 %
  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:  0.95 (0.30), residues: 788
  helix:  1.46 (0.26), residues: 402
  sheet: -0.18 (0.69), residues: 50
  loop : -0.17 (0.35), residues: 336

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   0.018   0.001   PHE C 490 
 TYR   0.016   0.001   TYR A 279 
 ARG   0.002   0.000   ARG A 219 

*********************** 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
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7900 (mtp) cc_final: 0.7626 (mpp)
REVERT: A  249 MET cc_start: 0.8390 (ptp) cc_final: 0.8007 (ttp)
REVERT: A  267 LEU cc_start: 0.8491 (mt) cc_final: 0.8193 (mt)
REVERT: A  270 MET cc_start: 0.8532 (tpt) cc_final: 0.7988 (tpt)
REVERT: A  350 ASP cc_start: 0.8065 (t0) cc_final: 0.7322 (p0)
REVERT: A  360 MET cc_start: 0.7931 (ptm) cc_final: 0.7586 (ptm)
REVERT: A  474 MET cc_start: 0.8514 (mmp) cc_final: 0.8184 (mmp)
REVERT: A  489 GLU cc_start: 0.8646 (pm20) cc_final: 0.8128 (pm20)
REVERT: C  396 TYR cc_start: 0.6933 (m-80) cc_final: 0.6311 (m-80)
REVERT: C  406 GLU cc_start: 0.8282 (tt0) cc_final: 0.8077 (tt0)
REVERT: C  489 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.5820 (p90)
REVERT: C  493 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6535 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 105
  average time/residue: 0.1568
  time to fit residues: 23.4984
Evaluate side-chains
  107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
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  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:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0030
   chunk 54 optimal weight:    0.0970
   chunk 65 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.9792

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.148317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.117706 restraints weight = 19064.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 3.66
r_work: 0.3068 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6649  Z= 0.162
  Angle     :  0.517   7.541   9042  Z= 0.262
  Chirality :  0.041   0.147    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.246  33.162    945
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.65 %
    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:  0.98 (0.30), residues: 788
  helix:  1.39 (0.26), residues: 408
  sheet: -0.17 (0.69), residues: 50
  loop : -0.04 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.013   0.001   PHE C 490 
 TYR   0.016   0.001   TYR A 279 
 ARG   0.002   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: 12
    poor density    : 100
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A   82 MET cc_start: 0.8076 (mtp) cc_final: 0.7769 (mpp)
REVERT: A  249 MET cc_start: 0.8462 (ptp) cc_final: 0.8085 (ttp)
REVERT: A  267 LEU cc_start: 0.8541 (mt) cc_final: 0.8256 (mt)
REVERT: A  270 MET cc_start: 0.8588 (tpt) cc_final: 0.7945 (tpt)
REVERT: A  350 ASP cc_start: 0.8146 (t0) cc_final: 0.7414 (p0)
REVERT: A  360 MET cc_start: 0.7962 (ptm) cc_final: 0.7646 (ptm)
REVERT: A  474 MET cc_start: 0.8573 (mmp) cc_final: 0.8240 (mmp)
REVERT: A  489 GLU cc_start: 0.8701 (pm20) cc_final: 0.8227 (pm20)
REVERT: C  396 TYR cc_start: 0.6953 (m-80) cc_final: 0.6341 (m-80)
REVERT: C  406 GLU cc_start: 0.8349 (tt0) cc_final: 0.8131 (tt0)
REVERT: C  484 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7440 (mm-30)
REVERT: C  489 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.5687 (p90)
REVERT: C  493 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6574 (tm-30)
  outliers start: 12
  outliers final: 8
  residues processed: 106
  average time/residue: 0.1487
  time to fit residues: 22.4528
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  : 0.670 
-------------------------------------------------------------------------------
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  324 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.145480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.111783 restraints weight = 14574.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.92
r_work: 0.3099 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3102
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6649  Z= 0.229
  Angle     :  0.556   7.382   9042  Z= 0.283
  Chirality :  0.042   0.157    959
  Planarity :  0.004   0.032   1169
  Dihedral  :  4.466  30.276    945
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.22 %
    Favored  : 84.05 %
  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:  0.78 (0.30), residues: 788
  helix:  1.21 (0.25), residues: 408
  sheet: -0.16 (0.69), residues: 50
  loop : -0.14 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 594 
 HIS   0.005   0.001   HIS A  34 
 PHE   0.017   0.001   PHE C 490 
 TYR   0.020   0.001   TYR A 279 
 ARG   0.003   0.001   ARG A 559 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3476.23 seconds
wall clock time: 62 minutes 22.50 seconds (3742.50 seconds total)