Starting phenix.real_space_refine
on Fri Jun  6 10:33:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c3y_16415/06_2025/8c3y_16415.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c3y_16415/06_2025/8c3y_16415.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c3y_16415/06_2025/8c3y_16415.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c3y_16415/06_2025/8c3y_16415.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c3y_16415/06_2025/8c3y_16415.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c3y_16415/06_2025/8c3y_16415.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.051
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    4777      2.51       5
     N    1319      2.21       5
     O    1441      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7580
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 929, 7580
          Classifications: {'peptide': 929}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 903}
          Chain breaks: 12
  Time building chain proxies: 4.71, per 1000 atoms: 0.62
  Number of scatterers: 7580
  At special positions: 0
  Unit cell: (74.88, 117.312, 107.328, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1441      8.00
     N    1319      7.00
     C    4777      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 109 " - pdb=" SG  CYS A 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 182 " - pdb=" SG  CYS A 281 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 310 " - pdb=" SG  CYS A 435 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 324 " - pdb=" SG  CYS A 359 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 356 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 340 " - pdb=" SG  CYS A 467 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 464 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 526 " - pdb=" SG  CYS A 614 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 542 " - pdb=" SG  CYS A 553 " distance=2.09
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 608 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 605 " - pdb=" SG  CYS A 719 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 612 " - pdb=" SG  CYS A 710 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 908 " - pdb=" SG  CYS A1000 " 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
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 959.4 milliseconds
  

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1756

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 3 sheets defined
      61.7% alpha, 2.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 42
      removed outlier: 3.853A  pdb=" N   LYS A  30 " --> pdb=" O   GLU A  26 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ASP A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ILE A  32 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 97
      removed outlier: 3.966A  pdb=" N   ARG A  95 " --> pdb=" O   PRO A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 134
    Processing helix  chain 'A' and resid 137 through 142
    Processing helix  chain 'A' and resid 150 through 172
    Processing helix  chain 'A' and resid 179 through 197
    Processing helix  chain 'A' and resid 212 through 227
    Processing helix  chain 'A' and resid 227 through 232
      removed outlier: 4.131A  pdb=" N   LEU A 231 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 256
      removed outlier: 5.536A  pdb=" N   GLU A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ASP A 250 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 324
    Processing helix  chain 'A' and resid 327 through 330
    Processing helix  chain 'A' and resid 356 through 393
      Proline residue:  A 365  - end of helix
    Processing helix  chain 'A' and resid 413 through 418
    Processing helix  chain 'A' and resid 421 through 431
      removed outlier: 4.190A  pdb=" N   GLU A 431 " --> pdb=" O   LYS A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 523
    Processing helix  chain 'A' and resid 523 through 528
    Processing helix  chain 'A' and resid 571 through 593
    Processing helix  chain 'A' and resid 593 through 598
    Processing helix  chain 'A' and resid 604 through 631
      removed outlier: 4.150A  pdb=" N   CYS A 608 " --> pdb=" O   ASP A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 644
    Processing helix  chain 'A' and resid 648 through 654
      removed outlier: 3.570A  pdb=" N   ASP A 652 " --> pdb=" O   ASP A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 659
    Processing helix  chain 'A' and resid 666 through 686
    Processing helix  chain 'A' and resid 690 through 713
      removed outlier: 3.932A  pdb=" N   ALA A 694 " --> pdb=" O   LYS A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 719
      removed outlier: 6.422A  pdb=" N   GLU A 717 " --> pdb=" O   ASN A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 763
    Processing helix  chain 'A' and resid 764 through 769
    Processing helix  chain 'A' and resid 844 through 848
    Processing helix  chain 'A' and resid 869 through 892
    Processing helix  chain 'A' and resid 904 through 924
    Processing helix  chain 'A' and resid 931 through 952
    Processing helix  chain 'A' and resid 954 through 962
      removed outlier: 3.882A  pdb=" N   ASN A 958 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   GLN A 959 " --> pdb=" O   LYS A 956 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   LYS A 960 " --> pdb=" O   ASP A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 967
    Processing helix  chain 'A' and resid 971 through 994
      removed outlier: 5.401A  pdb=" N   ASP A 984 " --> pdb=" O   GLU A 980 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   GLN A 985 " --> pdb=" O   ALA A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1040
    Processing helix  chain 'A' and resid 1058 through 1097
    Processing helix  chain 'A' and resid 1113 through 1126
    Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 267
    Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 326
    Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 509
      removed outlier: 7.006A  pdb=" N   GLN A 539 " --> pdb=" O   GLU A 556 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS A 552 " --> pdb=" O   TYR A 543 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1218 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: 2.09

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 1475
        1.32 -     1.46: 2542
        1.46 -     1.59: 3650
        1.59 -     1.73: 17
        1.73 -     1.87: 50
  Bond restraints: 7734
  Sorted by residual:
  bond pdb=" CB  TYR A 644 "
       pdb=" CG  TYR A 644 "
    ideal  model  delta    sigma   weight residual
    1.512  1.427  0.085 2.20e-02 2.07e+03 1.50e+01
  bond pdb=" NE  ARG A 215 "
       pdb=" CZ  ARG A 215 "
    ideal  model  delta    sigma   weight residual
    1.326  1.368 -0.042 1.10e-02 8.26e+03 1.44e+01
  bond pdb=" NE1 TRP A 589 "
       pdb=" CE2 TRP A 589 "
    ideal  model  delta    sigma   weight residual
    1.370  1.329  0.041 1.10e-02 8.26e+03 1.42e+01
  bond pdb=" CA  TYR A 543 "
       pdb=" C   TYR A 543 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.041 1.11e-02 8.12e+03 1.37e+01
  bond pdb=" CG  ASP A 964 "
       pdb=" OD2 ASP A 964 "
    ideal  model  delta    sigma   weight residual
    1.249  1.179  0.070 1.90e-02 2.77e+03 1.36e+01
  ... (remaining 7729 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 8194
        1.77 -     3.54: 1816
        3.54 -     5.32: 308
        5.32 -     7.09: 64
        7.09 -     8.86: 13
  Bond angle restraints: 10395
  Sorted by residual:
  angle pdb=" C   LEU A 841 "
        pdb=" N   PRO A 842 "
        pdb=" CA  PRO A 842 "
      ideal   model   delta    sigma   weight residual
     119.66  125.64   -5.98 7.30e-01 1.88e+00 6.72e+01
  angle pdb=" N   ILE A1166 "
        pdb=" CA  ILE A1166 "
        pdb=" C   ILE A1166 "
      ideal   model   delta    sigma   weight residual
     111.58  120.18   -8.60 1.06e+00 8.90e-01 6.58e+01
  angle pdb=" C   PRO A 842 "
        pdb=" N   PRO A 843 "
        pdb=" CA  PRO A 843 "
      ideal   model   delta    sigma   weight residual
     119.56  127.30   -7.74 1.02e+00 9.61e-01 5.75e+01
  angle pdb=" N   ILE A 559 "
        pdb=" CA  ILE A 559 "
        pdb=" C   ILE A 559 "
      ideal   model   delta    sigma   weight residual
     113.47  106.20    7.27 1.01e+00 9.80e-01 5.18e+01
  angle pdb=" C   MET A 952 "
        pdb=" N   PRO A 953 "
        pdb=" CA  PRO A 953 "
      ideal   model   delta    sigma   weight residual
     120.03  127.09   -7.06 9.90e-01 1.02e+00 5.08e+01
  ... (remaining 10390 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 4510
       17.87 -    35.74: 156
       35.74 -    53.61: 32
       53.61 -    71.48: 12
       71.48 -    89.35: 8
  Dihedral angle restraints: 4718
    sinusoidal: 2000
      harmonic: 2718
  Sorted by residual:
  dihedral pdb=" SG  CYS A 605 "
           pdb=" CB  CYS A 719 "
           pdb=" SG  CYS A 719 "
           pdb=" CA  CYS A 719 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    3.44   75.56     1      2.00e+01 2.50e-03 1.80e+01
  dihedral pdb=" CB  CYS A 340 "
           pdb=" SG  CYS A 340 "
           pdb=" SG  CYS A 467 "
           pdb=" CB  CYS A 467 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -55.46  -30.54     1      1.00e+01 1.00e-02 1.33e+01
  dihedral pdb=" CB  GLU A 515 "
           pdb=" CG  GLU A 515 "
           pdb=" CD  GLU A 515 "
           pdb=" OE1 GLU A 515 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.18   87.18     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 4715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 756
       0.096 -    0.191: 262
       0.191 -    0.287: 51
       0.287 -    0.383: 4
       0.383 -    0.479: 2
  Chirality restraints: 1075
  Sorted by residual:
  chirality pdb=" CB  VAL A 839 "
            pdb=" CA  VAL A 839 "
            pdb=" CG1 VAL A 839 "
            pdb=" CG2 VAL A 839 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.11    0.48 2.00e-01 2.50e+01 5.72e+00
  chirality pdb=" CB  VAL A 472 "
            pdb=" CA  VAL A 472 "
            pdb=" CG1 VAL A 472 "
            pdb=" CG2 VAL A 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.06    0.43 2.00e-01 2.50e+01 4.63e+00
  chirality pdb=" CA  ILE A 647 "
            pdb=" N   ILE A 647 "
            pdb=" C   ILE A 647 "
            pdb=" CB  ILE A 647 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.31 2.00e-01 2.50e+01 2.38e+00
  ... (remaining 1072 not shown)

  Planarity restraints: 1344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 544 "    0.081 2.00e-02 2.50e+03   4.43e-02 3.92e+01
        pdb=" CG  TYR A 544 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 544 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 544 "   -0.034 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 544 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 544 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 544 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 544 "    0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 669 "    0.058 2.00e-02 2.50e+03   2.90e-02 2.11e+01
        pdb=" CG  TRP A 669 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 669 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 669 "   -0.035 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 669 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 669 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 669 "   -0.039 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 669 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 669 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 669 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1017 "    0.371 9.50e-02 1.11e+02   1.66e-01 1.69e+01
        pdb=" NE  ARG A1017 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1017 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1017 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1017 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1341 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1479
        2.76 -     3.30: 7897
        3.30 -     3.83: 12979
        3.83 -     4.37: 15979
        4.37 -     4.90: 24659
  Nonbonded interactions: 62993
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 686 "
            pdb=" OG1 THR A 689 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG  SER A  20 "
            pdb=" ND2 ASN A  23 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" O   LEU A 645 "
            pdb=" ND2 ASN A 646 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" NZ  LYS A 745 "
            pdb=" OD1 ASP A1009 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" O   PHE A 651 "
            pdb=" O   PHE A 654 "
     model   vdw
     2.384 3.040
  ... (remaining 62988 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.810
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
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      :  0.018   0.100   7748  Z= 0.978
  Angle     :  1.565   8.860  10423  Z= 1.102
  Chirality :  0.097   0.479   1075
  Planarity :  0.010   0.166   1344
  Dihedral  : 10.954  89.353   2920
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.65 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  1.45 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.25), residues: 904
  helix:  0.93 (0.20), residues: 524
  sheet:  0.59 (1.04), residues: 23
  loop : -0.78 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.008   TRP A 669 
 HIS   0.007   0.002   HIS A 756 
 PHE   0.034   0.006   PHE A 615 
 TYR   0.081   0.008   TYR A 544 
 ARG   0.007   0.001   ARG A 983 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16097 (  431)
  hydrogen bonds       : angle       6.08688 ( 1218)
  SS BOND              : bond        0.01732 (   14)
  SS BOND              : angle       2.46812 (   28)
  covalent geometry    : bond        0.01802 ( 7734)
  covalent geometry    : angle       1.56194 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 294
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 LYS cc_start: 0.5720 (mttt) cc_final: 0.5253 (tttm)
REVERT: A  170 VAL cc_start: 0.7961 (m) cc_final: 0.7739 (m)
REVERT: A  256 THR cc_start: 0.8987 (p) cc_final: 0.8710 (t)
REVERT: A  291 ASN cc_start: 0.8715 (m-40) cc_final: 0.8486 (m-40)
REVERT: A  514 LYS cc_start: 0.8747 (tttt) cc_final: 0.8189 (tptm)
REVERT: A  647 ILE cc_start: 0.8356 (mt) cc_final: 0.8134 (mt)
REVERT: A  883 GLU cc_start: 0.8457 (tt0) cc_final: 0.8059 (pp20)
REVERT: A  912 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8578 (ttm110)
REVERT: A  991 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8450 (ttmt)
REVERT: A 1067 TYR cc_start: 0.9453 (t80) cc_final: 0.9000 (t80)
REVERT: A 1084 LYS cc_start: 0.9275 (mttt) cc_final: 0.9064 (mmtt)
  outliers start: 4
  outliers final: 0
  residues processed: 298
  average time/residue: 0.2707
  time to fit residues: 100.7239
Evaluate side-chains
  169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 ASN
A 364 ASN
A 380 GLN
A 621 GLN
A 648 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 871 HIS
A 958 ASN
A 967 ASN
A1070 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.110299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.086040 restraints weight = 20409.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.089670 restraints weight = 10872.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.092186 restraints weight = 7259.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7748  Z= 0.198
  Angle     :  0.743   9.366  10423  Z= 0.417
  Chirality :  0.045   0.185   1075
  Planarity :  0.005   0.059   1344
  Dihedral  :  4.845  20.574    995
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.21 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 10.64 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.27), residues: 904
  helix:  1.60 (0.21), residues: 523
  sheet:  0.20 (0.94), residues: 23
  loop : -0.61 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 244 
 HIS   0.009   0.001   HIS A  18 
 PHE   0.023   0.002   PHE A 458 
 TYR   0.024   0.002   TYR A 643 
 ARG   0.009   0.001   ARG A1017 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06851 (  431)
  hydrogen bonds       : angle       4.57307 ( 1218)
  SS BOND              : bond        0.00960 (   14)
  SS BOND              : angle       1.88997 (   28)
  covalent geometry    : bond        0.00422 ( 7734)
  covalent geometry    : angle       0.73800 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 194
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 GLU cc_start: 0.9176 (tp30) cc_final: 0.8889 (tp30)
REVERT: A  180 GLU cc_start: 0.8487 (tt0) cc_final: 0.7830 (tt0)
REVERT: A  243 TRP cc_start: 0.9087 (t60) cc_final: 0.8847 (t60)
REVERT: A  258 PHE cc_start: 0.8059 (m-80) cc_final: 0.7591 (m-80)
REVERT: A  307 ASP cc_start: 0.8660 (m-30) cc_final: 0.8360 (m-30)
REVERT: A  469 ASP cc_start: 0.8649 (m-30) cc_final: 0.8379 (t0)
REVERT: A  514 LYS cc_start: 0.9075 (tttt) cc_final: 0.8823 (tptm)
REVERT: A  555 MET cc_start: 0.6998 (mtp) cc_final: 0.6675 (mtp)
REVERT: A  595 TYR cc_start: 0.7830 (t80) cc_final: 0.7527 (t80)
REVERT: A  883 GLU cc_start: 0.8413 (tt0) cc_final: 0.7812 (pp20)
REVERT: A  912 ARG cc_start: 0.8518 (mtt180) cc_final: 0.7948 (ttm110)
REVERT: A  952 MET cc_start: 0.8304 (tpt) cc_final: 0.8039 (tpp)
  outliers start: 24
  outliers final: 16
  residues processed: 208
  average time/residue: 0.2392
  time to fit residues: 63.7486
Evaluate side-chains
  169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1098 ASN
Chi-restraints excluded: chain A residue 1117 ASP
Chi-restraints excluded: chain A residue 1126 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 12 optimal weight:    0.0060
   chunk 48 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8798

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 702 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.106643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.081609 restraints weight = 20751.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.085190 restraints weight = 10676.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.087648 restraints weight = 7096.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.4855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7748  Z= 0.167
  Angle     :  0.679   9.381  10423  Z= 0.369
  Chirality :  0.044   0.162   1075
  Planarity :  0.005   0.051   1344
  Dihedral  :  4.773  22.160    995
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.65 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 12.09 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.27), residues: 904
  helix:  1.51 (0.22), residues: 515
  sheet:  0.20 (0.97), residues: 23
  loop : -0.61 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 244 
 HIS   0.004   0.001   HIS A 173 
 PHE   0.033   0.002   PHE A1118 
 TYR   0.029   0.002   TYR A1067 
 ARG   0.007   0.001   ARG A 983 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05666 (  431)
  hydrogen bonds       : angle       4.44746 ( 1218)
  SS BOND              : bond        0.00429 (   14)
  SS BOND              : angle       1.37129 (   28)
  covalent geometry    : bond        0.00355 ( 7734)
  covalent geometry    : angle       0.67576 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 175
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 LYS cc_start: 0.9335 (mmmt) cc_final: 0.8567 (mmmt)
REVERT: A  137 ASP cc_start: 0.8537 (p0) cc_final: 0.8330 (p0)
REVERT: A  167 GLU cc_start: 0.9058 (tp30) cc_final: 0.8641 (mp0)
REVERT: A  180 GLU cc_start: 0.8595 (tt0) cc_final: 0.8258 (tt0)
REVERT: A  194 ASP cc_start: 0.9185 (m-30) cc_final: 0.8492 (m-30)
REVERT: A  260 ASP cc_start: 0.5593 (t70) cc_final: 0.5291 (t70)
REVERT: A  307 ASP cc_start: 0.8679 (m-30) cc_final: 0.8468 (m-30)
REVERT: A  469 ASP cc_start: 0.8809 (m-30) cc_final: 0.8496 (t0)
REVERT: A  514 LYS cc_start: 0.9223 (tttt) cc_final: 0.8852 (tptm)
REVERT: A  555 MET cc_start: 0.7541 (mtp) cc_final: 0.7180 (mtp)
REVERT: A  638 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7567 (p0)
REVERT: A  883 GLU cc_start: 0.8382 (tt0) cc_final: 0.7707 (pp20)
REVERT: A  912 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7824 (ttm110)
REVERT: A  913 TYR cc_start: 0.8930 (m-80) cc_final: 0.8488 (m-10)
REVERT: A  917 ASP cc_start: 0.9146 (m-30) cc_final: 0.8843 (m-30)
REVERT: A  952 MET cc_start: 0.8422 (tpt) cc_final: 0.8167 (tpp)
REVERT: A  963 ASP cc_start: 0.8748 (m-30) cc_final: 0.7629 (t0)
REVERT: A 1014 GLN cc_start: 0.8350 (tt0) cc_final: 0.7147 (mm-40)
REVERT: A 1018 TRP cc_start: 0.9136 (m-10) cc_final: 0.8430 (m100)
REVERT: A 1072 LYS cc_start: 0.9421 (pttm) cc_final: 0.9183 (pttm)
  outliers start: 35
  outliers final: 21
  residues processed: 195
  average time/residue: 0.2081
  time to fit residues: 53.5014
Evaluate side-chains
  171 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1064 CYS
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 ASP
Chi-restraints excluded: chain A residue 1126 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 134 HIS
A 175 ASN
A 393 HIS
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 749 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 = 0.3886 r_free = 0.3886 target = 0.106742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.082335 restraints weight = 20785.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.085758 restraints weight = 10928.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.088053 restraints weight = 7395.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.5482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7748  Z= 0.179
  Angle     :  0.639   8.885  10423  Z= 0.353
  Chirality :  0.043   0.152   1075
  Planarity :  0.005   0.081   1344
  Dihedral  :  4.618  20.117    995
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.98 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 14.51 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.28), residues: 904
  helix:  1.54 (0.21), residues: 517
  sheet:  0.01 (1.05), residues: 22
  loop : -0.59 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A 756 
 PHE   0.019   0.002   PHE A1118 
 TYR   0.028   0.002   TYR A1067 
 ARG   0.006   0.001   ARG A1017 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05209 (  431)
  hydrogen bonds       : angle       4.33409 ( 1218)
  SS BOND              : bond        0.00393 (   14)
  SS BOND              : angle       1.20465 (   28)
  covalent geometry    : bond        0.00384 ( 7734)
  covalent geometry    : angle       0.63646 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 160
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.9018 (tp30) cc_final: 0.8710 (mt-10)
REVERT: A  180 GLU cc_start: 0.8592 (tt0) cc_final: 0.8244 (tt0)
REVERT: A  307 ASP cc_start: 0.8475 (m-30) cc_final: 0.8260 (m-30)
REVERT: A  507 ASN cc_start: 0.8780 (p0) cc_final: 0.8391 (p0)
REVERT: A  514 LYS cc_start: 0.9169 (tttt) cc_final: 0.8807 (tptm)
REVERT: A  625 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6112 (mp0)
REVERT: A  638 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7590 (p0)
REVERT: A  883 GLU cc_start: 0.8335 (tt0) cc_final: 0.7682 (pp20)
REVERT: A  912 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8188 (ttm110)
REVERT: A  913 TYR cc_start: 0.8910 (m-80) cc_final: 0.8500 (m-10)
REVERT: A  917 ASP cc_start: 0.8976 (m-30) cc_final: 0.8552 (m-30)
REVERT: A  952 MET cc_start: 0.8269 (tpt) cc_final: 0.7943 (tpp)
REVERT: A  963 ASP cc_start: 0.8759 (m-30) cc_final: 0.7644 (t0)
REVERT: A 1014 GLN cc_start: 0.8494 (tt0) cc_final: 0.7380 (mm-40)
REVERT: A 1018 TRP cc_start: 0.9129 (m-10) cc_final: 0.8438 (m-10)
REVERT: A 1072 LYS cc_start: 0.9419 (pttm) cc_final: 0.9146 (pttm)
REVERT: A 1085 TYR cc_start: 0.8667 (t80) cc_final: 0.8458 (t80)
REVERT: A 1126 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8417 (t0)
REVERT: A 1130 LYS cc_start: 0.8876 (mttt) cc_final: 0.8493 (tmtt)
  outliers start: 34
  outliers final: 23
  residues processed: 182
  average time/residue: 0.2273
  time to fit residues: 54.2494
Evaluate side-chains
  173 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  758 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 ASP
Chi-restraints excluded: chain A residue 1126 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 702 HIS
** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.106845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.082584 restraints weight = 20464.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.085944 restraints weight = 11210.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.088183 restraints weight = 7671.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.5808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7748  Z= 0.144
  Angle     :  0.624   8.992  10423  Z= 0.337
  Chirality :  0.042   0.165   1075
  Planarity :  0.004   0.050   1344
  Dihedral  :  4.587  19.875    995
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.42 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 15.96 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.28), residues: 904
  helix:  1.57 (0.22), residues: 514
  sheet: -0.04 (1.05), residues: 24
  loop : -0.78 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 
 PHE   0.017   0.002   PHE A 220 
 TYR   0.023   0.002   TYR A1067 
 ARG   0.008   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04979 (  431)
  hydrogen bonds       : angle       4.31455 ( 1218)
  SS BOND              : bond        0.00348 (   14)
  SS BOND              : angle       1.04807 (   28)
  covalent geometry    : bond        0.00305 ( 7734)
  covalent geometry    : angle       0.62210 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 159
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 GLU cc_start: 0.8901 (pp20) cc_final: 0.8442 (pp20)
REVERT: A   42 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8878 (mmmt)
REVERT: A   98 ASN cc_start: 0.8931 (p0) cc_final: 0.8673 (p0)
REVERT: A  167 GLU cc_start: 0.8979 (tp30) cc_final: 0.8652 (mp0)
REVERT: A  180 GLU cc_start: 0.8543 (tt0) cc_final: 0.8236 (tt0)
REVERT: A  194 ASP cc_start: 0.9234 (m-30) cc_final: 0.8724 (m-30)
REVERT: A  258 PHE cc_start: 0.7719 (m-80) cc_final: 0.7514 (m-80)
REVERT: A  307 ASP cc_start: 0.8528 (m-30) cc_final: 0.8324 (m-30)
REVERT: A  507 ASN cc_start: 0.8822 (p0) cc_final: 0.8262 (p0)
REVERT: A  514 LYS cc_start: 0.9193 (tttt) cc_final: 0.8958 (tttp)
REVERT: A  625 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.5894 (mp0)
REVERT: A  630 MET cc_start: 0.8961 (mmp) cc_final: 0.8736 (mmp)
REVERT: A  673 LYS cc_start: 0.9109 (tttt) cc_final: 0.8845 (tptt)
REVERT: A  883 GLU cc_start: 0.8340 (tt0) cc_final: 0.7653 (pp20)
REVERT: A  912 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8125 (ttm110)
REVERT: A  913 TYR cc_start: 0.8910 (m-80) cc_final: 0.8525 (m-10)
REVERT: A  917 ASP cc_start: 0.9083 (m-30) cc_final: 0.8678 (m-30)
REVERT: A  952 MET cc_start: 0.8347 (tpt) cc_final: 0.8090 (tpp)
REVERT: A  963 ASP cc_start: 0.8755 (m-30) cc_final: 0.7620 (t0)
REVERT: A  980 GLU cc_start: 0.8670 (tp30) cc_final: 0.8461 (tp30)
REVERT: A 1014 GLN cc_start: 0.8386 (tt0) cc_final: 0.7313 (mm-40)
REVERT: A 1018 TRP cc_start: 0.9083 (m-10) cc_final: 0.8506 (m-10)
REVERT: A 1037 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9073 (mm)
REVERT: A 1072 LYS cc_start: 0.9412 (pttm) cc_final: 0.9152 (pttm)
REVERT: A 1085 TYR cc_start: 0.8673 (t80) cc_final: 0.8407 (t80)
REVERT: A 1130 LYS cc_start: 0.8871 (mttt) cc_final: 0.8467 (tmtt)
  outliers start: 33
  outliers final: 21
  residues processed: 180
  average time/residue: 0.2091
  time to fit residues: 50.4972
Evaluate side-chains
  167 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1095 TYR
Chi-restraints excluded: chain A residue 1117 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 12 optimal weight:    0.0070
   chunk 41 optimal weight:    0.8980
   chunk 85 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 8 optimal weight:    0.0670
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
A 175 ASN
A 417 ASN
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1126 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.107674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.083122 restraints weight = 20341.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.086482 restraints weight = 11236.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.088678 restraints weight = 7722.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.6092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7748  Z= 0.136
  Angle     :  0.611   9.711  10423  Z= 0.330
  Chirality :  0.041   0.155   1075
  Planarity :  0.004   0.037   1344
  Dihedral  :  4.535  19.118    995
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.65 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 18.26 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 904
  helix:  1.52 (0.22), residues: 518
  sheet: -0.42 (0.96), residues: 24
  loop : -0.86 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 
 PHE   0.016   0.002   PHE A 220 
 TYR   0.022   0.001   TYR A 643 
 ARG   0.007   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04754 (  431)
  hydrogen bonds       : angle       4.26216 ( 1218)
  SS BOND              : bond        0.00324 (   14)
  SS BOND              : angle       0.92413 (   28)
  covalent geometry    : bond        0.00284 ( 7734)
  covalent geometry    : angle       0.61004 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 161
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ASN cc_start: 0.8892 (p0) cc_final: 0.8647 (p0)
REVERT: A  167 GLU cc_start: 0.8967 (tp30) cc_final: 0.8671 (mp0)
REVERT: A  180 GLU cc_start: 0.8486 (tt0) cc_final: 0.8059 (mt-10)
REVERT: A  194 ASP cc_start: 0.9204 (m-30) cc_final: 0.8696 (m-30)
REVERT: A  387 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: A  507 ASN cc_start: 0.8833 (p0) cc_final: 0.8333 (p0)
REVERT: A  514 LYS cc_start: 0.9100 (tttt) cc_final: 0.8515 (ttmm)
REVERT: A  576 ASP cc_start: 0.8040 (m-30) cc_final: 0.7820 (m-30)
REVERT: A  625 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.5836 (mp0)
REVERT: A  630 MET cc_start: 0.9041 (mmp) cc_final: 0.8714 (mmp)
REVERT: A  638 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.7733 (p0)
REVERT: A  883 GLU cc_start: 0.8277 (tt0) cc_final: 0.7584 (pp20)
REVERT: A  913 TYR cc_start: 0.8897 (m-80) cc_final: 0.8541 (m-10)
REVERT: A  952 MET cc_start: 0.8356 (tpt) cc_final: 0.8111 (tpp)
REVERT: A  963 ASP cc_start: 0.8763 (m-30) cc_final: 0.7630 (t0)
REVERT: A  975 ARG cc_start: 0.8754 (mtm180) cc_final: 0.8322 (mtm180)
REVERT: A  982 ASN cc_start: 0.8896 (m-40) cc_final: 0.8599 (m110)
REVERT: A 1037 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8761 (mm)
REVERT: A 1067 TYR cc_start: 0.9378 (t80) cc_final: 0.9020 (t80)
REVERT: A 1072 LYS cc_start: 0.9364 (pttm) cc_final: 0.9121 (pttm)
REVERT: A 1130 LYS cc_start: 0.8926 (mttt) cc_final: 0.8505 (tmtt)
  outliers start: 31
  outliers final: 18
  residues processed: 180
  average time/residue: 0.2008
  time to fit residues: 48.1231
Evaluate side-chains
  166 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1095 TYR
Chi-restraints excluded: chain A residue 1117 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 46 optimal weight:    0.2980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 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 = 0.3864 r_free = 0.3864 target = 0.106327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.081715 restraints weight = 20858.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.085011 restraints weight = 11664.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.087197 restraints weight = 8079.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.6333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7748  Z= 0.160
  Angle     :  0.638  10.037  10423  Z= 0.347
  Chirality :  0.043   0.223   1075
  Planarity :  0.004   0.036   1344
  Dihedral  :  4.522  19.842    995
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.76 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 19.95 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.28), residues: 904
  helix:  1.66 (0.22), residues: 514
  sheet: -0.49 (0.92), residues: 22
  loop : -0.87 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 
 PHE   0.016   0.002   PHE A 220 
 TYR   0.025   0.002   TYR A 544 
 ARG   0.006   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04696 (  431)
  hydrogen bonds       : angle       4.28715 ( 1218)
  SS BOND              : bond        0.00317 (   14)
  SS BOND              : angle       0.96988 (   28)
  covalent geometry    : bond        0.00346 ( 7734)
  covalent geometry    : angle       0.63668 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ASN cc_start: 0.8891 (p0) cc_final: 0.8640 (p0)
REVERT: A  167 GLU cc_start: 0.8971 (tp30) cc_final: 0.8669 (mt-10)
REVERT: A  180 GLU cc_start: 0.8555 (tt0) cc_final: 0.8289 (tt0)
REVERT: A  194 ASP cc_start: 0.9141 (m-30) cc_final: 0.8633 (m-30)
REVERT: A  507 ASN cc_start: 0.8856 (p0) cc_final: 0.8322 (p0)
REVERT: A  514 LYS cc_start: 0.9265 (tttt) cc_final: 0.8652 (tttp)
REVERT: A  515 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7653 (mm-30)
REVERT: A  625 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.5784 (mp0)
REVERT: A  630 MET cc_start: 0.9029 (mmp) cc_final: 0.8769 (mmp)
REVERT: A  638 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.7702 (p0)
REVERT: A  883 GLU cc_start: 0.8279 (tt0) cc_final: 0.7574 (pp20)
REVERT: A  912 ARG cc_start: 0.8498 (mtt180) cc_final: 0.8094 (ttm110)
REVERT: A  952 MET cc_start: 0.8308 (tpt) cc_final: 0.8076 (tpp)
REVERT: A  963 ASP cc_start: 0.8750 (m-30) cc_final: 0.7610 (t0)
REVERT: A  982 ASN cc_start: 0.8974 (m-40) cc_final: 0.8709 (m110)
REVERT: A 1017 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7918 (mtm180)
REVERT: A 1067 TYR cc_start: 0.9403 (t80) cc_final: 0.9188 (t80)
REVERT: A 1072 LYS cc_start: 0.9341 (pttm) cc_final: 0.9094 (pttm)
REVERT: A 1130 LYS cc_start: 0.8958 (mttt) cc_final: 0.8515 (tmtt)
  outliers start: 31
  outliers final: 22
  residues processed: 174
  average time/residue: 0.2255
  time to fit residues: 51.9103
Evaluate side-chains
  163 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  758 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1095 TYR
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0270
   chunk 67 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0870
   chunk 34 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    1.2222

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 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 = 0.3855 r_free = 0.3855 target = 0.105705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.081320 restraints weight = 21254.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.084583 restraints weight = 11800.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.086774 restraints weight = 8171.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.6525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7748  Z= 0.164
  Angle     :  0.654  10.388  10423  Z= 0.356
  Chirality :  0.043   0.201   1075
  Planarity :  0.004   0.036   1344
  Dihedral  :  4.525  19.658    995
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.54 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.04 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.28), residues: 904
  helix:  1.59 (0.22), residues: 516
  sheet: -0.73 (0.91), residues: 24
  loop : -0.89 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.017   0.002   PHE A 220 
 TYR   0.020   0.002   TYR A 643 
 ARG   0.006   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04787 (  431)
  hydrogen bonds       : angle       4.35700 ( 1218)
  SS BOND              : bond        0.00311 (   14)
  SS BOND              : angle       0.93849 (   28)
  covalent geometry    : bond        0.00356 ( 7734)
  covalent geometry    : angle       0.65315 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ASN cc_start: 0.8900 (p0) cc_final: 0.8647 (p0)
REVERT: A  167 GLU cc_start: 0.8973 (tp30) cc_final: 0.8642 (mt-10)
REVERT: A  180 GLU cc_start: 0.8569 (tt0) cc_final: 0.8320 (tt0)
REVERT: A  194 ASP cc_start: 0.9070 (m-30) cc_final: 0.8569 (m-30)
REVERT: A  507 ASN cc_start: 0.8731 (p0) cc_final: 0.8268 (p0)
REVERT: A  514 LYS cc_start: 0.9277 (tttt) cc_final: 0.8570 (tttp)
REVERT: A  515 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7671 (mm-30)
REVERT: A  555 MET cc_start: 0.7390 (mpp) cc_final: 0.7077 (mpp)
REVERT: A  625 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5817 (mp0)
REVERT: A  630 MET cc_start: 0.9120 (mmp) cc_final: 0.8831 (mmp)
REVERT: A  673 LYS cc_start: 0.9126 (tttt) cc_final: 0.8903 (tmtt)
REVERT: A  758 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8894 (tt0)
REVERT: A  883 GLU cc_start: 0.8293 (tt0) cc_final: 0.7577 (pp20)
REVERT: A  912 ARG cc_start: 0.8581 (mtt180) cc_final: 0.8206 (ttm110)
REVERT: A  952 MET cc_start: 0.8306 (tpt) cc_final: 0.8078 (tpp)
REVERT: A  963 ASP cc_start: 0.8714 (m-30) cc_final: 0.7567 (t0)
REVERT: A  975 ARG cc_start: 0.8659 (mtm180) cc_final: 0.8383 (mtm180)
REVERT: A  982 ASN cc_start: 0.8953 (m-40) cc_final: 0.8692 (m110)
REVERT: A 1017 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8179 (mtm180)
REVERT: A 1067 TYR cc_start: 0.9443 (t80) cc_final: 0.9224 (t80)
REVERT: A 1072 LYS cc_start: 0.9320 (pttm) cc_final: 0.9086 (pttm)
REVERT: A 1084 LYS cc_start: 0.9427 (mmtt) cc_final: 0.9163 (mmtt)
REVERT: A 1130 LYS cc_start: 0.8963 (mttt) cc_final: 0.8504 (tmtt)
  outliers start: 24
  outliers final: 21
  residues processed: 166
  average time/residue: 0.2235
  time to fit residues: 49.6448
Evaluate side-chains
  166 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  758 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1095 TYR
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 91 optimal weight:    0.3980
   chunk 77 optimal weight:    0.2980
   chunk 35 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 HIS
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 ASN ** 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 = 0.3887 r_free = 0.3887 target = 0.107719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.082943 restraints weight = 20946.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.086321 restraints weight = 11615.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.088504 restraints weight = 8022.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.6746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7748  Z= 0.139
  Angle     :  0.642  10.393  10423  Z= 0.347
  Chirality :  0.043   0.204   1075
  Planarity :  0.004   0.036   1344
  Dihedral  :  4.438  19.752    995
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.87 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.52 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.28), residues: 904
  helix:  1.65 (0.22), residues: 506
  sheet: -0.59 (0.90), residues: 24
  loop : -0.72 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP A 244 
 HIS   0.002   0.001   HIS A  18 
 PHE   0.018   0.001   PHE A 654 
 TYR   0.018   0.001   TYR A 407 
 ARG   0.006   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04726 (  431)
  hydrogen bonds       : angle       4.30394 ( 1218)
  SS BOND              : bond        0.00287 (   14)
  SS BOND              : angle       0.87001 (   28)
  covalent geometry    : bond        0.00296 ( 7734)
  covalent geometry    : angle       0.64123 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 MET cc_start: 0.8611 (tpp) cc_final: 0.8178 (mmm)
REVERT: A   98 ASN cc_start: 0.8873 (p0) cc_final: 0.8632 (p0)
REVERT: A  167 GLU cc_start: 0.8984 (tp30) cc_final: 0.8681 (mt-10)
REVERT: A  180 GLU cc_start: 0.8561 (tt0) cc_final: 0.8214 (mt-10)
REVERT: A  227 ASN cc_start: 0.8951 (t0) cc_final: 0.8677 (t0)
REVERT: A  514 LYS cc_start: 0.9247 (tttt) cc_final: 0.8587 (tttp)
REVERT: A  515 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7650 (mm-30)
REVERT: A  625 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6345 (mp0)
REVERT: A  630 MET cc_start: 0.9121 (mmp) cc_final: 0.8860 (mmp)
REVERT: A  651 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7565 (p90)
REVERT: A  673 LYS cc_start: 0.9082 (tttt) cc_final: 0.8882 (tmtt)
REVERT: A  712 ASP cc_start: 0.8945 (t70) cc_final: 0.8614 (t70)
REVERT: A  774 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8649 (mmtm)
REVERT: A  883 GLU cc_start: 0.8213 (tt0) cc_final: 0.7538 (pp20)
REVERT: A  952 MET cc_start: 0.8261 (tpt) cc_final: 0.8051 (tpp)
REVERT: A  963 ASP cc_start: 0.8695 (m-30) cc_final: 0.7550 (t0)
REVERT: A  975 ARG cc_start: 0.8562 (mtm180) cc_final: 0.8274 (mtm180)
REVERT: A  982 ASN cc_start: 0.8926 (m-40) cc_final: 0.8661 (m110)
REVERT: A 1017 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8262 (mtm110)
REVERT: A 1067 TYR cc_start: 0.9427 (t80) cc_final: 0.9215 (t80)
REVERT: A 1072 LYS cc_start: 0.9288 (pttm) cc_final: 0.9078 (pttm)
REVERT: A 1084 LYS cc_start: 0.9457 (mmtt) cc_final: 0.9169 (mmtt)
REVERT: A 1130 LYS cc_start: 0.8918 (mttt) cc_final: 0.8468 (tmtt)
  outliers start: 19
  outliers final: 14
  residues processed: 164
  average time/residue: 0.2296
  time to fit residues: 50.0620
Evaluate side-chains
  166 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 1.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1095 TYR
Chi-restraints excluded: chain A residue 1117 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0470
   chunk 33 optimal weight:    0.4980
   chunk 43 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.9084

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 648 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 = 0.3875 r_free = 0.3875 target = 0.107060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.082716 restraints weight = 20814.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.086005 restraints weight = 11593.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.088208 restraints weight = 8036.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.6893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7748  Z= 0.148
  Angle     :  0.643  10.530  10423  Z= 0.347
  Chirality :  0.042   0.188   1075
  Planarity :  0.004   0.044   1344
  Dihedral  :  4.392  19.609    995
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.87 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.28 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.28), residues: 904
  helix:  1.61 (0.22), residues: 509
  sheet: -0.27 (0.95), residues: 24
  loop : -0.80 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.019   0.002   PHE A 458 
 TYR   0.020   0.001   TYR A 544 
 ARG   0.014   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04703 (  431)
  hydrogen bonds       : angle       4.28836 ( 1218)
  SS BOND              : bond        0.00298 (   14)
  SS BOND              : angle       0.85230 (   28)
  covalent geometry    : bond        0.00317 ( 7734)
  covalent geometry    : angle       0.64205 (10395)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 MET cc_start: 0.8636 (tpp) cc_final: 0.8200 (mmm)
REVERT: A   98 ASN cc_start: 0.8888 (p0) cc_final: 0.8647 (p0)
REVERT: A  167 GLU cc_start: 0.8994 (tp30) cc_final: 0.8735 (mt-10)
REVERT: A  180 GLU cc_start: 0.8620 (tt0) cc_final: 0.8220 (mt-10)
REVERT: A  191 ASP cc_start: 0.9514 (m-30) cc_final: 0.9165 (m-30)
REVERT: A  227 ASN cc_start: 0.8931 (t0) cc_final: 0.8668 (t0)
REVERT: A  514 LYS cc_start: 0.9264 (tttt) cc_final: 0.8590 (tttp)
REVERT: A  515 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7664 (mm-30)
REVERT: A  625 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5890 (mp0)
REVERT: A  630 MET cc_start: 0.9125 (mmp) cc_final: 0.8877 (mmp)
REVERT: A  758 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8911 (tt0)
REVERT: A  774 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8641 (mmtm)
REVERT: A  883 GLU cc_start: 0.8178 (tt0) cc_final: 0.7769 (tp30)
REVERT: A  912 ARG cc_start: 0.8609 (mtt180) cc_final: 0.8192 (ttm110)
REVERT: A  963 ASP cc_start: 0.8697 (m-30) cc_final: 0.7535 (t0)
REVERT: A  975 ARG cc_start: 0.8535 (mtm180) cc_final: 0.8236 (mtm180)
REVERT: A  982 ASN cc_start: 0.8967 (m-40) cc_final: 0.8707 (m110)
REVERT: A 1017 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8114 (mtm180)
REVERT: A 1067 TYR cc_start: 0.9431 (t80) cc_final: 0.9223 (t80)
REVERT: A 1072 LYS cc_start: 0.9281 (pttm) cc_final: 0.9069 (pttm)
REVERT: A 1084 LYS cc_start: 0.9461 (mmtt) cc_final: 0.9180 (mmtt)
REVERT: A 1130 LYS cc_start: 0.8922 (mttt) cc_final: 0.8447 (tmtt)
  outliers start: 22
  outliers final: 14
  residues processed: 167
  average time/residue: 0.2198
  time to fit residues: 48.6929
Evaluate side-chains
  161 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  758 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1095 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0070
   chunk 38 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 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 = 0.3882 r_free = 0.3882 target = 0.107646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.083458 restraints weight = 20880.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.086842 restraints weight = 11595.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.089074 restraints weight = 7972.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.7017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7748  Z= 0.140
  Angle     :  0.658  10.583  10423  Z= 0.353
  Chirality :  0.043   0.231   1075
  Planarity :  0.004   0.044   1344
  Dihedral  :  4.398  19.589    995
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.98 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.64 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.27), residues: 904
  helix:  1.61 (0.22), residues: 509
  sheet: -0.17 (0.96), residues: 24
  loop : -0.89 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP A 244 
 HIS   0.002   0.001   HIS A  18 
 PHE   0.027   0.002   PHE A 220 
 TYR   0.023   0.001   TYR A 643 
 ARG   0.016   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04647 (  431)
  hydrogen bonds       : angle       4.22689 ( 1218)
  SS BOND              : bond        0.00279 (   14)
  SS BOND              : angle       0.81515 (   28)
  covalent geometry    : bond        0.00296 ( 7734)
  covalent geometry    : angle       0.65745 (10395)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3275.25 seconds
wall clock time: 57 minutes 57.93 seconds (3477.93 seconds total)