Starting phenix.real_space_refine
on Tue Mar 11 17:48:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrk_21369/03_2025/6vrk_21369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrk_21369/03_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_21369/03_2025/6vrk_21369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrk_21369/03_2025/6vrk_21369.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrk_21369/03_2025/6vrk_21369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrk_21369/03_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-5624/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: 5.06, per 1000 atoms: 0.82
  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: 1.79
  Conformation dependent library (CDL) restraints added in 895.3 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: 0.72
  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: 1.64

  Time building geometry restraints manager: 1.98 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:             3.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.580
  Find NCS groups from input model:        0.060
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.470
-------------------------------------------------------------------------------
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  : 0.673 
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: 0.1834
  time to fit residues: 51.8016
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  : 0.613 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   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 101 ASN
A 238 GLN
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.184759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.164315 restraints weight = 11611.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.169042 restraints weight = 6994.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.172413 restraints weight = 4683.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.2280

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= 0.182
  Angle     :  0.628  13.930   8619  Z= 0.319
  Chirality :  0.040   0.152    966
  Planarity :  0.004   0.075   1048
  Dihedral  :  8.165  63.387    961
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  4.77 %
    Favored  : 94.77 %
  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: -2.01 (0.29), residues: 758
  helix: -0.09 (0.26), residues: 368
  sheet: -2.59 (0.46), residues: 89
  loop : -2.47 (0.35), residues: 301

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   0.028   0.002   PHE A 536 
 TYR   0.016   0.001   TYR B  52 
 ARG   0.005   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: 3
    poor density    : 181
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7693 (tmtt) cc_final: 0.7373 (tptp)
REVERT: A  107 TYR cc_start: 0.7821 (t80) cc_final: 0.7472 (t80)
REVERT: A  180 MET cc_start: 0.8804 (mmp) cc_final: 0.8491 (mmp)
REVERT: A  229 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8480 (tm-30)
REVERT: A  238 GLN cc_start: 0.6382 (tp40) cc_final: 0.6057 (mm-40)
REVERT: A  242 SER cc_start: 0.8466 (p) cc_final: 0.8249 (t)
REVERT: A  417 MET cc_start: 0.6486 (mtm) cc_final: 0.5904 (mtm)
REVERT: A  493 GLU cc_start: 0.6514 (tt0) cc_final: 0.6038 (mt-10)
REVERT: A  494 GLU cc_start: 0.8281 (tp30) cc_final: 0.7856 (tt0)
REVERT: A  563 LEU cc_start: 0.8510 (pt) cc_final: 0.5825 (tt)
REVERT: C  117 THR cc_start: 0.8094 (p) cc_final: 0.7857 (p)
REVERT: B  109 ASP cc_start: 0.7384 (m-30) cc_final: 0.7047 (m-30)
  outliers start: 3
  outliers final: 1
  residues processed: 182
  average time/residue: 0.1574
  time to fit residues: 38.9611
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  : 0.663 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 46 optimal weight:    0.2980
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
C  28 HIS
C 109 GLN
C 111 HIS
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.184875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.164877 restraints weight = 11861.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.169171 restraints weight = 7498.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.172249 restraints weight = 5206.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6326  Z= 0.191
  Angle     :  0.635  14.134   8619  Z= 0.321
  Chirality :  0.040   0.164    966
  Planarity :  0.004   0.069   1048
  Dihedral  :  7.903  58.482    961
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.38 %
    Favored  : 96.46 %
  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: -1.66 (0.30), residues: 758
  helix:  0.19 (0.26), residues: 369
  sheet: -2.50 (0.47), residues: 97
  loop : -2.24 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 458 
 HIS   0.002   0.001   HIS C 111 
 PHE   0.034   0.002   PHE A 373 
 TYR   0.018   0.002   TYR A 121 
 ARG   0.002   0.000   ARG C 116 

*********************** 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
  172 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7725 (tmtt) cc_final: 0.7397 (tptp)
REVERT: A  107 TYR cc_start: 0.7909 (t80) cc_final: 0.7587 (t80)
REVERT: A  152 ARG cc_start: 0.7050 (ttp-110) cc_final: 0.6132 (ttm-80)
REVERT: A  180 MET cc_start: 0.8793 (mmp) cc_final: 0.8351 (mmp)
REVERT: A  187 LEU cc_start: 0.8882 (tp) cc_final: 0.8676 (tp)
REVERT: A  229 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8524 (tm-30)
REVERT: A  242 SER cc_start: 0.8613 (p) cc_final: 0.8289 (t)
REVERT: A  306 TRP cc_start: 0.7163 (p-90) cc_final: 0.6166 (m-10)
REVERT: A  313 LEU cc_start: 0.8614 (mm) cc_final: 0.8113 (tt)
REVERT: A  410 TYR cc_start: 0.8502 (t80) cc_final: 0.7907 (t80)
REVERT: A  493 GLU cc_start: 0.6467 (tt0) cc_final: 0.6244 (tt0)
REVERT: A  494 GLU cc_start: 0.8187 (tp30) cc_final: 0.7828 (tt0)
REVERT: A  563 LEU cc_start: 0.8464 (pt) cc_final: 0.5721 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1664
  time to fit residues: 38.3157
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  : 0.607 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 11 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 GLN
C 109 GLN
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.181640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.161053 restraints weight = 12010.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.165592 restraints weight = 7394.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.168857 restraints weight = 5048.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6326  Z= 0.203
  Angle     :  0.667  16.507   8619  Z= 0.331
  Chirality :  0.041   0.165    966
  Planarity :  0.004   0.070   1048
  Dihedral  :  7.894  69.536    961
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  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: -1.45 (0.30), residues: 758
  helix:  0.36 (0.27), residues: 365
  sheet: -2.44 (0.46), residues: 101
  loop : -2.07 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 458 
 HIS   0.008   0.001   HIS C 111 
 PHE   0.025   0.002   PHE C 118 
 TYR   0.020   0.002   TYR B 114 
 ARG   0.004   0.000   ARG A 607 

*********************** 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
  169 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7710 (tmtt) cc_final: 0.7422 (tptp)
REVERT: A   88 PHE cc_start: 0.8365 (t80) cc_final: 0.8056 (t80)
REVERT: A  180 MET cc_start: 0.8842 (mmp) cc_final: 0.8331 (mmp)
REVERT: A  229 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8597 (tm-30)
REVERT: A  242 SER cc_start: 0.8669 (p) cc_final: 0.8424 (t)
REVERT: A  313 LEU cc_start: 0.8485 (mm) cc_final: 0.8151 (tp)
REVERT: A  410 TYR cc_start: 0.8559 (t80) cc_final: 0.8073 (t80)
REVERT: A  493 GLU cc_start: 0.6546 (tt0) cc_final: 0.6220 (tt0)
REVERT: A  563 LEU cc_start: 0.8556 (pt) cc_final: 0.7542 (tt)
REVERT: B  108 GLU cc_start: 0.7998 (pp20) cc_final: 0.7721 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1577
  time to fit residues: 36.2690
Evaluate side-chains
  137 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 64 optimal weight:    0.0170
   chunk 56 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 66 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 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 = 0.4243 r_free = 0.4243 target = 0.185031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.163941 restraints weight = 11835.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.168822 restraints weight = 7240.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.172149 restraints weight = 4896.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.3383

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= 0.160
  Angle     :  0.630  10.751   8619  Z= 0.316
  Chirality :  0.040   0.161    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  7.654  75.180    961
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  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: -1.17 (0.31), residues: 758
  helix:  0.54 (0.27), residues: 369
  sheet: -2.26 (0.47), residues: 101
  loop : -1.90 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP A 271 
 HIS   0.007   0.001   HIS C 111 
 PHE   0.024   0.001   PHE C 118 
 TYR   0.015   0.001   TYR B  79 
 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
  169 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7652 (tmtt) cc_final: 0.7314 (tptp)
REVERT: A  180 MET cc_start: 0.8863 (mmp) cc_final: 0.8308 (mmp)
REVERT: A  187 LEU cc_start: 0.8891 (tp) cc_final: 0.8675 (tp)
REVERT: A  229 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8564 (tm-30)
REVERT: A  242 SER cc_start: 0.8617 (p) cc_final: 0.8345 (t)
REVERT: A  306 TRP cc_start: 0.7165 (p-90) cc_final: 0.6060 (m-10)
REVERT: A  313 LEU cc_start: 0.8491 (mm) cc_final: 0.8040 (tp)
REVERT: A  314 LYS cc_start: 0.7220 (tttm) cc_final: 0.6925 (mtpt)
REVERT: A  410 TYR cc_start: 0.8275 (t80) cc_final: 0.7747 (t80)
REVERT: A  494 GLU cc_start: 0.8193 (tp30) cc_final: 0.7790 (tt0)
REVERT: A  563 LEU cc_start: 0.8566 (pt) cc_final: 0.6590 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1634
  time to fit residues: 37.8946
Evaluate side-chains
  137 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
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:    0.0570
   chunk 34 optimal weight:    0.0770
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 GLN
B 130 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.186678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.166970 restraints weight = 11237.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.171509 restraints weight = 6986.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.174678 restraints weight = 4762.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6326  Z= 0.152
  Angle     :  0.627  11.156   8619  Z= 0.315
  Chirality :  0.040   0.159    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  7.726  85.205    961
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  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: -1.06 (0.31), residues: 758
  helix:  0.60 (0.27), residues: 369
  sheet: -2.14 (0.46), residues: 101
  loop : -1.81 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 458 
 HIS   0.009   0.002   HIS A 143 
 PHE   0.030   0.001   PHE A 373 
 TYR   0.019   0.001   TYR A 267 
 ARG   0.002   0.000   ARG B 117 

*********************** 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
  170 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7634 (tmtt) cc_final: 0.7294 (tptp)
REVERT: A  180 MET cc_start: 0.8795 (mmp) cc_final: 0.8275 (mmp)
REVERT: A  187 LEU cc_start: 0.8860 (tp) cc_final: 0.8638 (tp)
REVERT: A  229 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8620 (tm-30)
REVERT: A  242 SER cc_start: 0.8510 (p) cc_final: 0.8233 (t)
REVERT: A  306 TRP cc_start: 0.7045 (p-90) cc_final: 0.6056 (m-10)
REVERT: A  313 LEU cc_start: 0.8492 (mm) cc_final: 0.8084 (tp)
REVERT: A  314 LYS cc_start: 0.7227 (tttm) cc_final: 0.6879 (mtpt)
REVERT: A  410 TYR cc_start: 0.8154 (t80) cc_final: 0.7261 (t80)
REVERT: A  493 GLU cc_start: 0.7022 (tt0) cc_final: 0.5930 (tt0)
REVERT: A  494 GLU cc_start: 0.8335 (tp30) cc_final: 0.7758 (tt0)
REVERT: A  528 MET cc_start: 0.7496 (ttm) cc_final: 0.7245 (ttm)
REVERT: A  563 LEU cc_start: 0.8610 (pt) cc_final: 0.6592 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1611
  time to fit residues: 37.8574
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  : 0.618 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 59 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 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 = 0.4233 r_free = 0.4233 target = 0.183858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.163266 restraints weight = 11825.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.167795 restraints weight = 7439.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.171022 restraints weight = 5152.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
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   0.038   6326  Z= 0.186
  Angle     :  0.659  12.151   8619  Z= 0.332
  Chirality :  0.041   0.148    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  7.804  85.845    961
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  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:  0.63 (0.27), residues: 369
  sheet: -2.08 (0.46), residues: 101
  loop : -1.62 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP A 541 
 HIS   0.009   0.002   HIS C 111 
 PHE   0.023   0.002   PHE A 548 
 TYR   0.012   0.002   TYR A 267 
 ARG   0.005   0.000   ARG A 538 

*********************** 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
  163 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7598 (tmtt) cc_final: 0.7217 (tptp)
REVERT: A  144 ARG cc_start: 0.6824 (mtp180) cc_final: 0.6427 (mtt180)
REVERT: A  180 MET cc_start: 0.8859 (mmp) cc_final: 0.8266 (mmp)
REVERT: A  229 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8550 (tm-30)
REVERT: A  242 SER cc_start: 0.8617 (p) cc_final: 0.8371 (t)
REVERT: A  306 TRP cc_start: 0.7228 (p-90) cc_final: 0.6057 (m-10)
REVERT: A  313 LEU cc_start: 0.8610 (mm) cc_final: 0.8089 (tt)
REVERT: A  314 LYS cc_start: 0.7285 (tttm) cc_final: 0.6873 (mtpt)
REVERT: A  410 TYR cc_start: 0.8022 (t80) cc_final: 0.7485 (t80)
REVERT: A  432 ILE cc_start: 0.8754 (mt) cc_final: 0.8497 (mt)
REVERT: A  493 GLU cc_start: 0.7062 (tt0) cc_final: 0.5978 (tt0)
REVERT: A  494 GLU cc_start: 0.8418 (tp30) cc_final: 0.7856 (tt0)
REVERT: A  528 MET cc_start: 0.7497 (ttm) cc_final: 0.7223 (ttm)
REVERT: A  563 LEU cc_start: 0.8660 (pt) cc_final: 0.6682 (tt)
REVERT: C   75 TYR cc_start: 0.8133 (t80) cc_final: 0.7906 (t80)
REVERT: C  109 GLN cc_start: 0.7404 (tt0) cc_final: 0.6217 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1555
  time to fit residues: 35.0278
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  : 0.597 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0870
   chunk 28 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
A 112 ASN
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.186351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.166330 restraints weight = 11740.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.170594 restraints weight = 7505.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.173679 restraints weight = 5268.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.3946

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= 0.159
  Angle     :  0.630  11.965   8619  Z= 0.318
  Chirality :  0.041   0.153    966
  Planarity :  0.004   0.075   1048
  Dihedral  :  7.854  89.910    961
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: -0.76 (0.31), residues: 758
  helix:  0.76 (0.27), residues: 368
  sheet: -2.08 (0.47), residues: 101
  loop : -1.50 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 541 
 HIS   0.003   0.001   HIS C 111 
 PHE   0.025   0.001   PHE A 287 
 TYR   0.020   0.001   TYR A 267 
 ARG   0.002   0.000   ARG B 117 

*********************** 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
  166 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7608 (tmtt) cc_final: 0.7219 (tptp)
REVERT: A  144 ARG cc_start: 0.6772 (mtp180) cc_final: 0.6457 (mtt-85)
REVERT: A  180 MET cc_start: 0.8871 (mmp) cc_final: 0.8275 (mmp)
REVERT: A  187 LEU cc_start: 0.8901 (tp) cc_final: 0.8656 (tp)
REVERT: A  229 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8511 (tm-30)
REVERT: A  242 SER cc_start: 0.8551 (p) cc_final: 0.8278 (t)
REVERT: A  306 TRP cc_start: 0.7148 (p-90) cc_final: 0.6167 (m-10)
REVERT: A  313 LEU cc_start: 0.8561 (mm) cc_final: 0.8084 (tt)
REVERT: A  314 LYS cc_start: 0.7256 (tttm) cc_final: 0.6850 (mtpt)
REVERT: A  410 TYR cc_start: 0.7992 (t80) cc_final: 0.7268 (t80)
REVERT: A  432 ILE cc_start: 0.8763 (mt) cc_final: 0.8541 (mt)
REVERT: A  493 GLU cc_start: 0.7043 (tt0) cc_final: 0.6031 (tt0)
REVERT: A  494 GLU cc_start: 0.8376 (tp30) cc_final: 0.7891 (tt0)
REVERT: A  528 MET cc_start: 0.7488 (ttm) cc_final: 0.7206 (ttm)
REVERT: A  562 GLN cc_start: 0.6939 (tp-100) cc_final: 0.6710 (tp40)
REVERT: A  563 LEU cc_start: 0.8600 (pt) cc_final: 0.6446 (tt)
REVERT: B  133 THR cc_start: 0.7853 (p) cc_final: 0.7573 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1509
  time to fit residues: 34.7923
Evaluate side-chains
  143 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 61 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 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 = 0.4250 r_free = 0.4250 target = 0.184714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.164772 restraints weight = 11434.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.169127 restraints weight = 7250.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.172226 restraints weight = 5019.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6326  Z= 0.168
  Angle     :  0.641  12.716   8619  Z= 0.323
  Chirality :  0.041   0.150    966
  Planarity :  0.004   0.075   1048
  Dihedral  :  7.429  79.754    961
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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:  0.79 (0.27), residues: 368
  sheet: -2.10 (0.46), residues: 101
  loop : -1.40 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP A 541 
 HIS   0.008   0.001   HIS C 111 
 PHE   0.025   0.002   PHE A 548 
 TYR   0.020   0.002   TYR A 267 
 ARG   0.003   0.000   ARG B 117 

*********************** 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
  167 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7602 (tmtt) cc_final: 0.7210 (tptp)
REVERT: A  144 ARG cc_start: 0.6810 (mtp180) cc_final: 0.6470 (mtt-85)
REVERT: A  180 MET cc_start: 0.8846 (mmp) cc_final: 0.8250 (mmp)
REVERT: A  187 LEU cc_start: 0.8879 (tp) cc_final: 0.8645 (tp)
REVERT: A  229 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8498 (tm-30)
REVERT: A  242 SER cc_start: 0.8526 (p) cc_final: 0.8242 (t)
REVERT: A  306 TRP cc_start: 0.7155 (p-90) cc_final: 0.6146 (m-10)
REVERT: A  313 LEU cc_start: 0.8617 (mm) cc_final: 0.8079 (tt)
REVERT: A  314 LYS cc_start: 0.7294 (tttm) cc_final: 0.7053 (ttpp)
REVERT: A  410 TYR cc_start: 0.7837 (t80) cc_final: 0.7459 (t80)
REVERT: A  432 ILE cc_start: 0.8736 (mt) cc_final: 0.8523 (mt)
REVERT: A  437 ASP cc_start: 0.7641 (p0) cc_final: 0.7407 (p0)
REVERT: A  493 GLU cc_start: 0.7078 (tt0) cc_final: 0.6225 (tt0)
REVERT: A  494 GLU cc_start: 0.8369 (tp30) cc_final: 0.7879 (tt0)
REVERT: A  528 MET cc_start: 0.7398 (ttm) cc_final: 0.7184 (ttm)
REVERT: A  563 LEU cc_start: 0.8583 (pt) cc_final: 0.6422 (tt)
REVERT: B  133 THR cc_start: 0.7909 (p) cc_final: 0.7658 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1458
  time to fit residues: 33.8179
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  : 0.651 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 57 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS
B 130 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.191060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.169451 restraints weight = 11923.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.174333 restraints weight = 7160.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.177791 restraints weight = 4838.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6868
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6326  Z= 0.170
  Angle     :  0.649  12.293   8619  Z= 0.328
  Chirality :  0.041   0.192    966
  Planarity :  0.005   0.076   1048
  Dihedral  :  7.322  76.932    961
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.31 %
    Favored  : 99.54 %
  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: -0.65 (0.31), residues: 758
  helix:  0.82 (0.27), residues: 369
  sheet: -2.02 (0.47), residues: 101
  loop : -1.42 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.067   0.002   TRP A 541 
 HIS   0.003   0.001   HIS C 111 
 PHE   0.026   0.002   PHE A 548 
 TYR   0.027   0.002   TYR A 267 
 ARG   0.008   0.000   ARG B 117 

********************** 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: 1
    poor density    : 164
  time to evaluate  : 0.623 
Fit side-chains
REVERT: A   85 LYS cc_start: 0.7623 (tmtt) cc_final: 0.7272 (tptp)
REVERT: A  144 ARG cc_start: 0.6779 (mtp180) cc_final: 0.6435 (mtt-85)
REVERT: A  180 MET cc_start: 0.8811 (mmp) cc_final: 0.8250 (mmp)
REVERT: A  187 LEU cc_start: 0.8863 (tp) cc_final: 0.8628 (tp)
REVERT: A  229 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: A  242 SER cc_start: 0.8512 (p) cc_final: 0.8254 (t)
REVERT: A  306 TRP cc_start: 0.7180 (p-90) cc_final: 0.6175 (m-10)
REVERT: A  313 LEU cc_start: 0.8606 (mm) cc_final: 0.8064 (tt)
REVERT: A  314 LYS cc_start: 0.7307 (tttm) cc_final: 0.7056 (ttpp)
REVERT: A  410 TYR cc_start: 0.7809 (t80) cc_final: 0.7556 (t80)
REVERT: A  432 ILE cc_start: 0.8784 (mt) cc_final: 0.8549 (mt)
REVERT: A  437 ASP cc_start: 0.7647 (p0) cc_final: 0.7385 (p0)
REVERT: A  493 GLU cc_start: 0.6993 (tt0) cc_final: 0.6267 (tt0)
REVERT: A  494 GLU cc_start: 0.8360 (tp30) cc_final: 0.7887 (tt0)
REVERT: A  528 MET cc_start: 0.7421 (ttm) cc_final: 0.7210 (ttm)
REVERT: A  563 LEU cc_start: 0.8430 (pt) cc_final: 0.6450 (tt)
REVERT: B  133 THR cc_start: 0.7895 (p) cc_final: 0.7627 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 165
  average time/residue: 0.1459
  time to fit residues: 33.5591
Evaluate side-chains
  143 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 65 optimal weight:    0.0470
   chunk 55 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   overall best weight:    1.4882

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 GLN
B 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.187228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.166721 restraints weight = 12253.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.171210 restraints weight = 7684.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.174308 restraints weight = 5294.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.4307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6326  Z= 0.204
  Angle     :  0.674  13.163   8619  Z= 0.341
  Chirality :  0.042   0.161    966
  Planarity :  0.005   0.076   1048
  Dihedral  :  6.938  61.057    961
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.77 %
    Favored  : 99.08 %
  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:  0.81 (0.27), residues: 365
  sheet: -1.97 (0.48), residues: 101
  loop : -1.45 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.002   TRP A 541 
 HIS   0.010   0.002   HIS C 111 
 PHE   0.026   0.002   PHE A 536 
 TYR   0.017   0.002   TYR B  52 
 ARG   0.009   0.001   ARG B 117 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2432.74 seconds
wall clock time: 42 minutes 52.65 seconds (2572.65 seconds total)