Starting phenix.real_space_refine
on Tue Feb 11 18:21:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrk_21369/02_2025/6vrk_21369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrk_21369/02_2025/6vrk_21369.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrk_21369/02_2025/6vrk_21369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrk_21369/02_2025/6vrk_21369.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrk_21369/02_2025/6vrk_21369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrk_21369/02_2025/6vrk_21369.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.975
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Br      1      7.06       5
     S      34      5.16       5
     C    4045      2.51       5
     N     958      2.21       5
     O    1103      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 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: 6141
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4311
          Classifications: {'peptide': 541}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 23, 'TRANS': 517}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100}
    Chain: "B"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 924
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 5, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 87
          Unusual residues: {'LMT': 1, 'NAG': 2, 'RFS': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.38, per 1000 atoms: 0.88
  Number of scatterers: 6141
  At special positions: 0
  Unit cell: (97.2, 102.384, 82.296, 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)
     Br      1     34.99
     S      34     16.00
     O    1103      8.00
     N     958      7.00
     C    4045      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " 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 701 " - " ASN A 208 "
      " NAG A 702 " - " ASN A 217 "
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 845.1 milliseconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 7 sheets defined
      56.3% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 4.271A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A  89 " --> pdb=" O   LYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 112
      removed outlier: 4.976A  pdb=" N   PHE A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 129 through 144
    Processing helix  chain 'A' and resid 148 through 154
      removed outlier: 4.000A  pdb=" N   TRP A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.016A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 271
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 4.056A  pdb=" N   LYS A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TRP A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 300
      removed outlier: 3.724A  pdb=" N   ILE A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 314
      removed outlier: 3.945A  pdb=" N   GLY A 308 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 4.064A  pdb=" N   TRP A 326 " --> pdb=" O   GLU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
    Processing helix  chain 'A' and resid 356 through 390
      removed outlier: 3.653A  pdb=" N   VAL A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 398
      removed outlier: 3.921A  pdb=" N   VAL A 397 " --> pdb=" O   ASP A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 408
    Processing helix  chain 'A' and resid 408 through 416
    Processing helix  chain 'A' and resid 419 through 454
      removed outlier: 4.170A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 478
      removed outlier: 3.538A  pdb=" N   VAL A 469 " --> pdb=" O   PHE A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 495
      removed outlier: 4.287A  pdb=" N   VAL A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 515
    Processing helix  chain 'A' and resid 517 through 529
    Processing helix  chain 'A' and resid 534 through 543
    Processing helix  chain 'A' and resid 543 through 557
    Processing helix  chain 'A' and resid 571 through 584
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 4.044A  pdb=" N   THR A 591 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TYR A 592 " --> pdb=" O   CYS A 588 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A 593 " --> pdb=" O   ILE A 589 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU A 597 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A 599 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR A 600 " --> pdb=" O   ARG A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 613
      removed outlier: 3.653A  pdb=" N   ARG A 607 " --> pdb=" O   THR A 603 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   THR A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 3.978A  pdb=" N   TYR B  51 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 96
    Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565
    Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 26
    Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 41
      removed outlier: 3.646A  pdb=" N   ASP C  90 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 73 through 74
      removed outlier: 6.794A  pdb=" N   TRP C  55 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   TYR C  69 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR C 107 " --> pdb=" O   TYR C  56 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN C  58 " --> pdb=" O   VAL C 105 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL C 105 " --> pdb=" O   GLN C  58 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 30
      removed outlier: 5.743A  pdb=" N   GLU B  29 " --> pdb=" O   THR B 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38
    Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 68
      removed outlier: 6.627A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER B 118 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL B  56 " --> pdb=" O   TYR B 114 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR B 114 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)

    304 hydrogen bonds defined for protein.
    855 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: 2.00

  Time building geometry restraints manager: 1.87 seconds

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

  Histogram of bond lengths:
        1.23 -     1.36: 1822
        1.36 -     1.49: 1931
        1.49 -     1.63: 2523
        1.63 -     1.76: 0
        1.76 -     1.89: 50
  Bond restraints: 6326
  Sorted by residual:
  bond pdb=" C06 RFS A 704 "
       pdb=" C07 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.511  1.602 -0.091 2.00e-02 2.50e+03 2.07e+01
  bond pdb=" C14 RFS A 704 "
       pdb=" O15 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.432  1.499 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C16 RFS A 704 "
       pdb=" O15 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.362  1.426 -0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" C07 RFS A 704 "
       pdb=" C08 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.394  1.456 -0.062 2.00e-02 2.50e+03 9.53e+00
  bond pdb=" C19 RFS A 704 "
       pdb=" C20 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.376  1.437 -0.061 2.00e-02 2.50e+03 9.17e+00
  ... (remaining 6321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 8493
        2.32 -     4.64: 98
        4.64 -     6.97: 18
        6.97 -     9.29: 9
        9.29 -    11.61: 1
  Bond angle restraints: 8619
  Sorted by residual:
  angle pdb=" C   VAL B 120 "
        pdb=" N   ARG B 121 "
        pdb=" CA  ARG B 121 "
      ideal   model   delta    sigma   weight residual
     121.80  133.41  -11.61 2.44e+00 1.68e-01 2.26e+01
  angle pdb=" N   ILE A 587 "
        pdb=" CA  ILE A 587 "
        pdb=" C   ILE A 587 "
      ideal   model   delta    sigma   weight residual
     112.98  107.67    5.31 1.25e+00 6.40e-01 1.81e+01
  angle pdb=" N   ARG B 121 "
        pdb=" CA  ARG B 121 "
        pdb=" C   ARG B 121 "
      ideal   model   delta    sigma   weight residual
     109.81  117.87   -8.06 2.21e+00 2.05e-01 1.33e+01
  angle pdb=" C2  LMT A 703 "
        pdb=" C3  LMT A 703 "
        pdb=" C4  LMT A 703 "
      ideal   model   delta    sigma   weight residual
     117.09  107.89    9.20 3.00e+00 1.11e-01 9.40e+00
  angle pdb=" C   TRP A 458 "
        pdb=" N   ALA A 459 "
        pdb=" CA  ALA A 459 "
      ideal   model   delta    sigma   weight residual
     121.54  127.20   -5.66 1.91e+00 2.74e-01 8.78e+00
  ... (remaining 8614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 3320
       17.44 -    34.87: 300
       34.87 -    52.31: 51
       52.31 -    69.75: 12
       69.75 -    87.18: 9
  Dihedral angle restraints: 3692
    sinusoidal: 1478
      harmonic: 2214
  Sorted by residual:
  dihedral pdb=" CA  ARG B 121 "
           pdb=" C   ARG B 121 "
           pdb=" N   PRO B 122 "
           pdb=" CA  PRO B 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.50   44.50     0      5.00e+00 4.00e-02 7.92e+01
  dihedral pdb=" CB  CYS C  43 "
           pdb=" SG  CYS C  43 "
           pdb=" SG  CYS C 108 "
           pdb=" CB  CYS C 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -33.27  -52.73     1      1.00e+01 1.00e-02 3.79e+01
  dihedral pdb=" CA  TYR B 123 "
           pdb=" C   TYR B 123 "
           pdb=" N   TYR B 124 "
           pdb=" CA  TYR B 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.46   18.54     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 3689 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 724
       0.042 -    0.083: 196
       0.083 -    0.125: 40
       0.125 -    0.167: 2
       0.167 -    0.208: 4
  Chirality restraints: 966
  Sorted by residual:
  chirality pdb=" C5' LMT A 703 "
            pdb=" C4' LMT A 703 "
            pdb=" C6' LMT A 703 "
            pdb=" O5' LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.30   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" C3B LMT A 703 "
            pdb=" C2B LMT A 703 "
            pdb=" C4B LMT A 703 "
            pdb=" O3B LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.29    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C4' LMT A 703 "
            pdb=" C3' LMT A 703 "
            pdb=" C5' LMT A 703 "
            pdb=" O1B LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.76    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 963 not shown)

  Planarity restraints: 1050
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 121 "   -0.043 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO B 122 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B 122 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 122 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 548 "    0.012 2.00e-02 2.50e+03   9.45e-03 1.56e+00
        pdb=" CG  PHE A 548 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 548 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 548 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 548 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 548 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 548 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 130 "    0.020 5.00e-02 4.00e+02   3.08e-02 1.51e+00
        pdb=" N   PRO A 131 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 131 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 131 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1047 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1363
        2.78 -     3.31: 6145
        3.31 -     3.84: 10436
        3.84 -     4.37: 11804
        4.37 -     4.90: 20067
  Nonbonded interactions: 49815
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 596 "
            pdb=" OG1 THR A 600 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG1 THR C  51 "
            pdb=" O   SER C  70 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR A 385 "
            pdb=" OD1 ASN A 416 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG1 THR C  83 "
            pdb=" O   THR C  94 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG1 THR A 210 "
            pdb=" OG  SER A 224 "
     model   vdw
     2.268 3.040
  ... (remaining 49810 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             10.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          1.320
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     18.910
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
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      :  0.004   0.091   6326  Z= 0.246
  Angle     :  0.686  11.612   8619  Z= 0.350
  Chirality :  0.040   0.208    966
  Planarity :  0.004   0.065   1048
  Dihedral  : 13.927  87.184   2277
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -3.10 (0.27), residues: 758
  helix: -1.01 (0.23), residues: 359
  sheet: -3.09 (0.42), residues: 89
  loop : -2.93 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 103 
 HIS   0.005   0.001   HIS C 111 
 PHE   0.021   0.001   PHE A 548 
 TYR   0.014   0.001   TYR B 123 
 ARG   0.002   0.000   ARG A 152 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7388 (tptp)
REVERT: A  135 MET cc_start: 0.9118 (tmm) cc_final: 0.8871 (tmm)
REVERT: A  152 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6490 (ttm-80)
REVERT: A  229 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8683 (tm-30)
REVERT: A  417 MET cc_start: 0.6445 (mtm) cc_final: 0.5830 (mtm)
REVERT: A  432 ILE cc_start: 0.8960 (mt) cc_final: 0.8707 (mt)
REVERT: A  493 GLU cc_start: 0.6717 (tt0) cc_final: 0.6314 (tt0)
REVERT: A  494 GLU cc_start: 0.8033 (tp30) cc_final: 0.7783 (tt0)
REVERT: A  563 LEU cc_start: 0.8343 (pt) cc_final: 0.6023 (tt)
REVERT: C   48 ASP cc_start: 0.7048 (t0) cc_final: 0.6770 (t0)
REVERT: C   99 GLN cc_start: 0.6118 (mt0) cc_final: 0.5802 (mt0)
REVERT: B   58 GLN cc_start: 0.6535 (tm-30) cc_final: 0.6331 (tm-30)
REVERT: B  109 ASP cc_start: 0.7275 (m-30) cc_final: 0.6728 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1973
  time to fit residues: 55.2625
Evaluate side-chains
  159 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 31 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 30 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 238 GLN
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
C 109 GLN
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.183399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.164035 restraints weight = 11474.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.168482 restraints weight = 7015.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.171545 restraints weight = 4720.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6326  Z= 0.189
  Angle     :  0.630  13.917   8619  Z= 0.320
  Chirality :  0.040   0.160    966
  Planarity :  0.004   0.075   1048
  Dihedral  :  8.294  67.877    961
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  5.54 %
    Favored  : 94.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -2.07 (0.29), residues: 758
  helix: -0.11 (0.26), residues: 367
  sheet: -2.55 (0.46), residues: 86
  loop : -2.58 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 541 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.024   0.002   PHE A 548 
 TYR   0.016   0.001   TYR B  52 
 ARG   0.006   0.001   ARG A 152 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7689 (tmtt) cc_final: 0.7390 (tptp)
REVERT: A  107 TYR cc_start: 0.7813 (t80) cc_final: 0.7474 (t80)
REVERT: A  180 MET cc_start: 0.8847 (mmp) cc_final: 0.8526 (mmp)
REVERT: A  238 GLN cc_start: 0.6378 (tp40) cc_final: 0.6023 (mm-40)
REVERT: A  242 SER cc_start: 0.8486 (p) cc_final: 0.8262 (t)
REVERT: A  417 MET cc_start: 0.6520 (mtm) cc_final: 0.5941 (mtm)
REVERT: A  493 GLU cc_start: 0.6527 (tt0) cc_final: 0.6021 (mt-10)
REVERT: A  494 GLU cc_start: 0.8323 (tp30) cc_final: 0.7900 (tt0)
REVERT: A  563 LEU cc_start: 0.8537 (pt) cc_final: 0.5836 (tt)
REVERT: C  117 THR cc_start: 0.8137 (p) cc_final: 0.7902 (p)
REVERT: B  109 ASP cc_start: 0.7405 (m-30) cc_final: 0.7141 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 183
  average time/residue: 0.1812
  time to fit residues: 44.1842
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 70 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 HIS
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
C  28 HIS
** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.181747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.161572 restraints weight = 11943.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.165933 restraints weight = 7454.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.169063 restraints weight = 5131.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6326  Z= 0.215
  Angle     :  0.658  15.181   8619  Z= 0.332
  Chirality :  0.041   0.167    966
  Planarity :  0.005   0.070   1048
  Dihedral  :  8.143  56.565    961
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.74 (0.30), residues: 758
  helix:  0.15 (0.27), residues: 368
  sheet: -2.56 (0.47), residues: 97
  loop : -2.30 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 541 
 HIS   0.003   0.001   HIS C 111 
 PHE   0.022   0.002   PHE A 548 
 TYR   0.018   0.002   TYR B 114 
 ARG   0.002   0.000   ARG B 117 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7738 (tmtt) cc_final: 0.7480 (tptp)
REVERT: A   88 PHE cc_start: 0.8239 (t80) cc_final: 0.7997 (t80)
REVERT: A  107 TYR cc_start: 0.7970 (t80) cc_final: 0.7651 (t80)
REVERT: A  152 ARG cc_start: 0.7110 (ttp-110) cc_final: 0.6156 (ttm-80)
REVERT: A  180 MET cc_start: 0.8843 (mmp) cc_final: 0.8474 (mmp)
REVERT: A  229 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: A  242 SER cc_start: 0.8689 (p) cc_final: 0.8367 (t)
REVERT: A  306 TRP cc_start: 0.7245 (p-90) cc_final: 0.6231 (m-10)
REVERT: A  410 TYR cc_start: 0.8534 (t80) cc_final: 0.7828 (t80)
REVERT: A  417 MET cc_start: 0.6574 (mtm) cc_final: 0.6344 (mtm)
REVERT: A  493 GLU cc_start: 0.6509 (tt0) cc_final: 0.6191 (tt0)
REVERT: A  494 GLU cc_start: 0.8245 (tp30) cc_final: 0.7859 (tt0)
REVERT: A  570 TYR cc_start: 0.7957 (m-80) cc_final: 0.7622 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.1688
  time to fit residues: 40.7782
Evaluate side-chains
  150 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 3 optimal weight:    0.7980
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.175098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.155338 restraints weight = 11901.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.159533 restraints weight = 7418.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.162294 restraints weight = 5109.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6326  Z= 0.299
  Angle     :  0.741  13.631   8619  Z= 0.381
  Chirality :  0.043   0.186    966
  Planarity :  0.005   0.074   1048
  Dihedral  :  8.538  57.268    961
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -2.00 (0.30), residues: 758
  helix: -0.06 (0.26), residues: 370
  sheet: -2.70 (0.44), residues: 101
  loop : -2.43 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 458 
 HIS   0.008   0.002   HIS C 111 
 PHE   0.038   0.003   PHE C 118 
 TYR   0.025   0.002   TYR B 114 
 ARG   0.004   0.001   ARG B 117 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7758 (tmtt) cc_final: 0.7460 (tptp)
REVERT: A  229 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8610 (tm-30)
REVERT: A  242 SER cc_start: 0.8794 (p) cc_final: 0.8542 (t)
REVERT: A  313 LEU cc_start: 0.8595 (mm) cc_final: 0.8230 (tp)
REVERT: A  314 LYS cc_start: 0.7453 (tttm) cc_final: 0.7166 (ttpp)
REVERT: A  410 TYR cc_start: 0.8552 (t80) cc_final: 0.8043 (t80)
REVERT: A  570 TYR cc_start: 0.8100 (m-80) cc_final: 0.7736 (m-80)
REVERT: B  108 GLU cc_start: 0.7754 (pp20) cc_final: 0.7474 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1631
  time to fit residues: 39.2378
Evaluate side-chains
  146 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.180650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.160153 restraints weight = 11723.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.164522 restraints weight = 7261.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.167719 restraints weight = 4975.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6326  Z= 0.177
  Angle     :  0.660  11.284   8619  Z= 0.335
  Chirality :  0.041   0.148    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  7.990  64.782    961
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.08 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.54 (0.30), residues: 758
  helix:  0.26 (0.27), residues: 373
  sheet: -2.50 (0.44), residues: 101
  loop : -2.10 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 271 
 HIS   0.013   0.003   HIS C 111 
 PHE   0.023   0.002   PHE A 373 
 TYR   0.020   0.002   TYR B 114 
 ARG   0.002   0.000   ARG B 117 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7650 (tmtt) cc_final: 0.7389 (tptp)
REVERT: A  107 TYR cc_start: 0.8107 (t80) cc_final: 0.7851 (t80)
REVERT: A  180 MET cc_start: 0.9063 (mmp) cc_final: 0.8853 (mmp)
REVERT: A  185 TYR cc_start: 0.7566 (t80) cc_final: 0.7281 (t80)
REVERT: A  187 LEU cc_start: 0.8858 (tp) cc_final: 0.8644 (tp)
REVERT: A  229 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8577 (tm-30)
REVERT: A  238 GLN cc_start: 0.6416 (mm-40) cc_final: 0.5941 (mm-40)
REVERT: A  242 SER cc_start: 0.8664 (p) cc_final: 0.8406 (t)
REVERT: A  313 LEU cc_start: 0.8552 (mm) cc_final: 0.8218 (tp)
REVERT: A  410 TYR cc_start: 0.8235 (t80) cc_final: 0.7951 (t80)
REVERT: A  563 LEU cc_start: 0.8608 (pt) cc_final: 0.7703 (tt)
REVERT: A  570 TYR cc_start: 0.8005 (m-80) cc_final: 0.7785 (m-80)
REVERT: C   75 TYR cc_start: 0.8367 (t80) cc_final: 0.8114 (t80)
REVERT: B  108 GLU cc_start: 0.7699 (pp20) cc_final: 0.7487 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1682
  time to fit residues: 40.7664
Evaluate side-chains
  147 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    0.0470
   chunk 34 optimal weight:    0.0970
   chunk 6 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0030
   chunk 26 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.3686

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.183546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.163981 restraints weight = 11532.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.168349 restraints weight = 7120.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.171468 restraints weight = 4845.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6326  Z= 0.157
  Angle     :  0.658  11.296   8619  Z= 0.327
  Chirality :  0.041   0.149    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  7.912  75.062    961
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.23 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.14 (0.31), residues: 758
  helix:  0.47 (0.27), residues: 370
  sheet: -2.40 (0.43), residues: 101
  loop : -1.67 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 458 
 HIS   0.009   0.002   HIS C 111 
 PHE   0.021   0.001   PHE A 521 
 TYR   0.017   0.001   TYR A 267 
 ARG   0.002   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7595 (tmtt) cc_final: 0.7360 (tptp)
REVERT: A  107 TYR cc_start: 0.8028 (t80) cc_final: 0.7774 (t80)
REVERT: A  180 MET cc_start: 0.9060 (mmp) cc_final: 0.8801 (mmp)
REVERT: A  187 LEU cc_start: 0.8856 (tp) cc_final: 0.8647 (tp)
REVERT: A  229 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8586 (tm-30)
REVERT: A  242 SER cc_start: 0.8539 (p) cc_final: 0.8224 (t)
REVERT: A  313 LEU cc_start: 0.8511 (mm) cc_final: 0.8226 (tp)
REVERT: A  410 TYR cc_start: 0.8291 (t80) cc_final: 0.7968 (t80)
REVERT: A  417 MET cc_start: 0.4624 (mmm) cc_final: 0.3756 (tpp)
REVERT: A  432 ILE cc_start: 0.8815 (mt) cc_final: 0.8595 (mt)
REVERT: A  493 GLU cc_start: 0.6650 (tt0) cc_final: 0.6074 (tt0)
REVERT: A  563 LEU cc_start: 0.8731 (pt) cc_final: 0.7605 (tt)
REVERT: C   75 TYR cc_start: 0.8213 (t80) cc_final: 0.7941 (t80)
REVERT: B  113 TYR cc_start: 0.7561 (m-10) cc_final: 0.7273 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 169
  average time/residue: 0.1624
  time to fit residues: 36.9802
Evaluate side-chains
  138 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0270
   chunk 29 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6840

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 GLN
** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.184413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.163518 restraints weight = 11913.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.168196 restraints weight = 7276.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.171519 restraints weight = 4942.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6326  Z= 0.160
  Angle     :  0.632  10.328   8619  Z= 0.321
  Chirality :  0.041   0.154    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  7.717  82.995    961
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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 (0.31), residues: 758
  helix:  0.58 (0.27), residues: 372
  sheet: -2.32 (0.43), residues: 101
  loop : -1.45 (0.40), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 271 
 HIS   0.012   0.001   HIS A 143 
 PHE   0.019   0.001   PHE A 536 
 TYR   0.015   0.001   TYR A 358 
 ARG   0.003   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7672 (tmtt) cc_final: 0.7395 (tptp)
REVERT: A  180 MET cc_start: 0.9018 (mmp) cc_final: 0.8773 (mmt)
REVERT: A  187 LEU cc_start: 0.8879 (tp) cc_final: 0.8669 (tp)
REVERT: A  229 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8589 (tm-30)
REVERT: A  238 GLN cc_start: 0.5983 (tp-100) cc_final: 0.5740 (tp-100)
REVERT: A  242 SER cc_start: 0.8490 (p) cc_final: 0.8188 (t)
REVERT: A  306 TRP cc_start: 0.7101 (p-90) cc_final: 0.6087 (m-10)
REVERT: A  313 LEU cc_start: 0.8388 (mm) cc_final: 0.8098 (tp)
REVERT: A  410 TYR cc_start: 0.8117 (t80) cc_final: 0.7586 (t80)
REVERT: A  417 MET cc_start: 0.4304 (mmm) cc_final: 0.3633 (tpp)
REVERT: A  432 ILE cc_start: 0.8882 (mt) cc_final: 0.8644 (mt)
REVERT: A  493 GLU cc_start: 0.6647 (tt0) cc_final: 0.6149 (tt0)
REVERT: A  563 LEU cc_start: 0.8677 (pt) cc_final: 0.7553 (tt)
REVERT: C   75 TYR cc_start: 0.8218 (t80) cc_final: 0.7983 (t80)
REVERT: B  108 GLU cc_start: 0.7667 (pp20) cc_final: 0.7441 (pp20)
REVERT: B  113 TYR cc_start: 0.7547 (m-10) cc_final: 0.7298 (m-10)
REVERT: B  133 THR cc_start: 0.7912 (p) cc_final: 0.7616 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1632
  time to fit residues: 37.1269
Evaluate side-chains
  145 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    0.0040
   chunk 40 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 16 optimal weight:    0.0980
   chunk 28 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  28 HIS
** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.187000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.167028 restraints weight = 11812.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.171336 restraints weight = 7459.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.174391 restraints weight = 5187.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6326  Z= 0.156
  Angle     :  0.644  10.793   8619  Z= 0.322
  Chirality :  0.040   0.157    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  7.667  88.000    961
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.31), residues: 758
  helix:  0.64 (0.27), residues: 373
  sheet: -2.26 (0.44), residues: 101
  loop : -1.42 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 458 
 HIS   0.005   0.001   HIS A 143 
 PHE   0.027   0.002   PHE A 287 
 TYR   0.023   0.001   TYR A 267 
 ARG   0.002   0.000   ARG A  79 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A   85 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7304 (tptp)
REVERT: A  180 MET cc_start: 0.9026 (mmp) cc_final: 0.8790 (mmp)
REVERT: A  187 LEU cc_start: 0.8878 (tp) cc_final: 0.8644 (tp)
REVERT: A  229 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8547 (tm-30)
REVERT: A  238 GLN cc_start: 0.5923 (tp-100) cc_final: 0.5699 (tp-100)
REVERT: A  242 SER cc_start: 0.8464 (p) cc_final: 0.8205 (t)
REVERT: A  306 TRP cc_start: 0.7121 (p-90) cc_final: 0.6044 (m-10)
REVERT: A  410 TYR cc_start: 0.8156 (t80) cc_final: 0.7651 (t80)
REVERT: A  417 MET cc_start: 0.3986 (mmm) cc_final: 0.3311 (tpp)
REVERT: A  437 ASP cc_start: 0.7666 (p0) cc_final: 0.7452 (p0)
REVERT: A  493 GLU cc_start: 0.6643 (tt0) cc_final: 0.6080 (tt0)
REVERT: A  494 GLU cc_start: 0.8334 (tp30) cc_final: 0.7637 (tt0)
REVERT: A  563 LEU cc_start: 0.8636 (pt) cc_final: 0.6585 (tt)
REVERT: C   75 TYR cc_start: 0.8178 (t80) cc_final: 0.7919 (t80)
REVERT: B  133 THR cc_start: 0.7902 (p) cc_final: 0.7598 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1614
  time to fit residues: 36.4061
Evaluate side-chains
  141 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    0.0370
   chunk 50 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 48 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** 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 = 0.4261 r_free = 0.4261 target = 0.186739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.166635 restraints weight = 11942.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.170963 restraints weight = 7660.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.174037 restraints weight = 5359.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6326  Z= 0.163
  Angle     :  0.633  10.350   8619  Z= 0.320
  Chirality :  0.041   0.156    966
  Planarity :  0.004   0.070   1048
  Dihedral  :  7.319  81.004    961
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -0.74 (0.31), residues: 758
  helix:  0.74 (0.27), residues: 372
  sheet: -2.19 (0.45), residues: 101
  loop : -1.41 (0.40), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.067   0.002   TRP A 541 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.024   0.002   PHE A 556 
 TYR   0.024   0.001   TYR A 267 
 ARG   0.002   0.000   ARG A  79 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.632 
Fit side-chains
REVERT: A   85 LYS cc_start: 0.7694 (tmtt) cc_final: 0.7344 (tptp)
REVERT: A  180 MET cc_start: 0.9003 (mmp) cc_final: 0.8766 (mmp)
REVERT: A  187 LEU cc_start: 0.8854 (tp) cc_final: 0.8625 (tp)
REVERT: A  229 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8510 (tm-30)
REVERT: A  238 GLN cc_start: 0.6006 (tp-100) cc_final: 0.5778 (tp-100)
REVERT: A  242 SER cc_start: 0.8478 (p) cc_final: 0.8172 (t)
REVERT: A  306 TRP cc_start: 0.7134 (p-90) cc_final: 0.6118 (m-10)
REVERT: A  410 TYR cc_start: 0.7953 (t80) cc_final: 0.7454 (t80)
REVERT: A  417 MET cc_start: 0.3976 (mmm) cc_final: 0.3647 (tpp)
REVERT: A  432 ILE cc_start: 0.8875 (mt) cc_final: 0.8603 (mt)
REVERT: A  493 GLU cc_start: 0.6674 (tt0) cc_final: 0.6137 (tt0)
REVERT: A  562 GLN cc_start: 0.6975 (tp-100) cc_final: 0.6719 (tp40)
REVERT: A  563 LEU cc_start: 0.8609 (pt) cc_final: 0.7372 (tt)
REVERT: C   75 TYR cc_start: 0.8138 (t80) cc_final: 0.7900 (t80)
REVERT: B  133 THR cc_start: 0.7911 (p) cc_final: 0.7624 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1588
  time to fit residues: 35.5014
Evaluate side-chains
  142 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** 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 = 0.4252 r_free = 0.4252 target = 0.185528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.163999 restraints weight = 11910.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.168705 restraints weight = 7391.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.172079 restraints weight = 5097.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6326  Z= 0.176
  Angle     :  0.658  10.987   8619  Z= 0.331
  Chirality :  0.041   0.152    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  7.140  79.440    961
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -0.69 (0.31), residues: 758
  helix:  0.82 (0.27), residues: 369
  sheet: -2.14 (0.46), residues: 101
  loop : -1.43 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP A 541 
 HIS   0.009   0.001   HIS C 111 
 PHE   0.020   0.001   PHE A 536 
 TYR   0.023   0.001   TYR A 267 
 ARG   0.002   0.000   ARG A  79 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7687 (tmtt) cc_final: 0.7329 (tptp)
REVERT: A  180 MET cc_start: 0.8980 (mmp) cc_final: 0.8642 (mmp)
REVERT: A  187 LEU cc_start: 0.8893 (tp) cc_final: 0.8678 (tp)
REVERT: A  229 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8519 (tm-30)
REVERT: A  238 GLN cc_start: 0.6229 (tp-100) cc_final: 0.5907 (tp-100)
REVERT: A  242 SER cc_start: 0.8489 (p) cc_final: 0.8192 (t)
REVERT: A  306 TRP cc_start: 0.7215 (p-90) cc_final: 0.6185 (m-10)
REVERT: A  314 LYS cc_start: 0.7576 (tttt) cc_final: 0.6958 (mtpt)
REVERT: A  410 TYR cc_start: 0.7959 (t80) cc_final: 0.7475 (t80)
REVERT: A  417 MET cc_start: 0.3929 (mmm) cc_final: 0.3630 (tpp)
REVERT: A  432 ILE cc_start: 0.8917 (mt) cc_final: 0.8626 (mt)
REVERT: A  437 ASP cc_start: 0.7771 (p0) cc_final: 0.7567 (p0)
REVERT: A  493 GLU cc_start: 0.6678 (tt0) cc_final: 0.6286 (tt0)
REVERT: A  562 GLN cc_start: 0.6998 (tp-100) cc_final: 0.6793 (tp40)
REVERT: A  563 LEU cc_start: 0.8642 (pt) cc_final: 0.7405 (tt)
REVERT: C   75 TYR cc_start: 0.8188 (t80) cc_final: 0.7942 (t80)
REVERT: B  108 GLU cc_start: 0.7633 (pp20) cc_final: 0.7431 (pp20)
REVERT: B  133 THR cc_start: 0.7960 (p) cc_final: 0.7678 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1563
  time to fit residues: 35.3207
Evaluate side-chains
  142 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 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 = 0.4220 r_free = 0.4220 target = 0.182248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.160956 restraints weight = 12209.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.165613 restraints weight = 7624.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.168912 restraints weight = 5266.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6326  Z= 0.219
  Angle     :  0.682  11.132   8619  Z= 0.346
  Chirality :  0.042   0.150    966
  Planarity :  0.005   0.071   1048
  Dihedral  :  7.162  69.146    961
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -0.70 (0.31), residues: 758
  helix:  0.79 (0.27), residues: 369
  sheet: -2.19 (0.47), residues: 99
  loop : -1.38 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.002   TRP A 541 
 HIS   0.002   0.001   HIS A 240 
 PHE   0.025   0.002   PHE A 287 
 TYR   0.024   0.002   TYR A 267 
 ARG   0.012   0.001   ARG B 117 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2360.01 seconds
wall clock time: 44 minutes 25.54 seconds (2665.54 seconds total)