Starting phenix.real_space_refine
on Fri Aug 22 20:16:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c3y_16415/08_2025/8c3y_16415.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c3y_16415/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c3y_16415/08_2025/8c3y_16415.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c3y_16415/08_2025/8c3y_16415.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c3y_16415/08_2025/8c3y_16415.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c3y_16415/08_2025/8c3y_16415.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.45, per 1000 atoms: 0.19
  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: 0.42
  Conformation dependent library (CDL) restraints added in 293.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.15
  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: 0.79

  Time building geometry restraints manager: 0.60 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:             2.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.580
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.170
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.001   ARG A 983 
 TYR   0.081   0.008   TYR A 544 
 PHE   0.034   0.006   PHE A 615 
 TRP   0.058   0.008   TRP A 669 
 HIS   0.007   0.002   HIS A 756 

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

*********************** 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  : 0.306 
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: A  163 LYS cc_start: 0.5720 (mttt) cc_final: 0.5230 (tttm)
REVERT: A  170 VAL cc_start: 0.7961 (m) cc_final: 0.7730 (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: 0.8345 (m110)
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: 0.9024 (t80)
  outliers start: 4
  outliers final: 0
  residues processed: 298
  average time/residue: 0.1072
  time to fit residues: 40.1339
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  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 149 GLN
** 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: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.109517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.084963 restraints weight = 20848.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.088574 restraints weight = 11095.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.091009 restraints weight = 7431.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.092734 restraints weight = 5707.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.093886 restraints weight = 4744.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   7748  Z= 0.229
  Angle     :  0.754   9.408  10423  Z= 0.426
  Chirality :  0.045   0.189   1075
  Planarity :  0.005   0.060   1344
  Dihedral  :  4.858  20.710    995
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.21 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 10.64 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.27), residues: 904
  helix:  1.52 (0.21), residues: 527
  sheet:  0.27 (0.95), residues: 23
  loop : -0.67 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 300 
 TYR   0.024   0.002   TYR A 643 
 PHE   0.024   0.002   PHE A 458 
 TRP   0.030   0.002   TRP A 244 
 HIS   0.008   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 7734)
  covalent geometry    : angle       0.74987 (10395)
  SS BOND              : bond        0.00601 (   14)
  SS BOND              : angle       1.77477 (   28)
  hydrogen bonds       : bond        0.06897 (  431)
  hydrogen bonds       : angle       4.61702 ( 1218)

*********************** 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
  217 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 190
  time to evaluate  : 0.335 
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: A  180 GLU cc_start: 0.8488 (tt0) cc_final: 0.8014 (tt0)
REVERT: A  243 TRP cc_start: 0.9095 (t60) cc_final: 0.8825 (t60)
REVERT: A  307 ASP cc_start: 0.8683 (m-30) cc_final: 0.8381 (m-30)
REVERT: A  514 LYS cc_start: 0.9073 (tttt) cc_final: 0.8828 (tptm)
REVERT: A  555 MET cc_start: 0.6886 (mtp) cc_final: 0.6591 (mtp)
REVERT: A  595 TYR cc_start: 0.7823 (t80) cc_final: 0.7512 (t80)
REVERT: A  841 LEU cc_start: 0.9204 (pt) cc_final: 0.8927 (tt)
REVERT: A  873 LEU cc_start: 0.8595 (tp) cc_final: 0.8387 (tp)
REVERT: A  883 GLU cc_start: 0.8394 (tt0) cc_final: 0.7995 (tp30)
REVERT: A  912 ARG cc_start: 0.8499 (mtt180) cc_final: 0.7889 (ttm110)
REVERT: A  952 MET cc_start: 0.8342 (tpt) cc_final: 0.8016 (tpp)
REVERT: A 1086 LYS cc_start: 0.9636 (mttt) cc_final: 0.9377 (mmtt)
  outliers start: 27
  outliers final: 18
  residues processed: 207
  average time/residue: 0.1003
  time to fit residues: 26.8347
Evaluate side-chains
  170 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
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  168 SER
Chi-restraints excluded: chain A residue  179 SER
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 0 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 ** 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 = 0.3833 r_free = 0.3833 target = 0.106184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.081109 restraints weight = 20652.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.084635 restraints weight = 10738.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.087073 restraints weight = 7150.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.088745 restraints weight = 5471.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.089770 restraints weight = 4584.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7748  Z= 0.171
  Angle     :  0.681   9.388  10423  Z= 0.373
  Chirality :  0.044   0.152   1075
  Planarity :  0.005   0.049   1344
  Dihedral  :  4.757  21.892    995
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.65 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 12.58 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.28), residues: 904
  helix:  1.51 (0.22), residues: 512
  sheet:  0.05 (0.97), residues: 21
  loop : -0.63 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 300 
 TYR   0.027   0.002   TYR A1067 
 PHE   0.034   0.002   PHE A1118 
 TRP   0.036   0.002   TRP A 244 
 HIS   0.006   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7734)
  covalent geometry    : angle       0.67860 (10395)
  SS BOND              : bond        0.00312 (   14)
  SS BOND              : angle       1.34001 (   28)
  hydrogen bonds       : bond        0.05651 (  431)
  hydrogen bonds       : angle       4.43441 ( 1218)

*********************** 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
  202 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 172
  time to evaluate  : 0.344 
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   42 LYS cc_start: 0.9344 (mmmt) cc_final: 0.8623 (mmmt)
REVERT: A  137 ASP cc_start: 0.8530 (p0) cc_final: 0.8320 (p0)
REVERT: A  167 GLU cc_start: 0.9122 (tp30) cc_final: 0.8675 (mt-10)
REVERT: A  180 GLU cc_start: 0.8535 (tt0) cc_final: 0.8103 (tt0)
REVERT: A  194 ASP cc_start: 0.9118 (m-30) cc_final: 0.8433 (m-30)
REVERT: A  307 ASP cc_start: 0.8661 (m-30) cc_final: 0.8454 (m-30)
REVERT: A  469 ASP cc_start: 0.8790 (m-30) cc_final: 0.8467 (t0)
REVERT: A  514 LYS cc_start: 0.9235 (tttt) cc_final: 0.8865 (tptm)
REVERT: A  555 MET cc_start: 0.7467 (mtp) cc_final: 0.7124 (mtp)
REVERT: A  638 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7515 (p0)
REVERT: A  673 LYS cc_start: 0.9080 (tttt) cc_final: 0.8831 (tptt)
REVERT: A  841 LEU cc_start: 0.9300 (pt) cc_final: 0.8877 (tt)
REVERT: A  883 GLU cc_start: 0.8371 (tt0) cc_final: 0.7693 (pp20)
REVERT: A  912 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7792 (ttm110)
REVERT: A  913 TYR cc_start: 0.8913 (m-80) cc_final: 0.8586 (m-10)
REVERT: A  952 MET cc_start: 0.8346 (tpt) cc_final: 0.7949 (tpp)
REVERT: A  963 ASP cc_start: 0.8730 (m-30) cc_final: 0.7592 (t0)
REVERT: A 1032 LYS cc_start: 0.9486 (ttpp) cc_final: 0.9264 (ptmm)
REVERT: A 1072 LYS cc_start: 0.9418 (pttm) cc_final: 0.9166 (pttm)
REVERT: A 1086 LYS cc_start: 0.9639 (mttt) cc_final: 0.9394 (mmtt)
  outliers start: 30
  outliers final: 21
  residues processed: 188
  average time/residue: 0.0927
  time to fit residues: 23.1374
Evaluate side-chains
  170 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  220 PHE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  429 LEU
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  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 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 60 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 75 optimal weight:    0.2980
   chunk 73 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0970
   chunk 80 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.109237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.085147 restraints weight = 20750.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.088734 restraints weight = 10636.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.091153 restraints weight = 7046.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.092759 restraints weight = 5393.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.093738 restraints weight = 4501.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.5394

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= 0.142
  Angle     :  0.618   8.742  10423  Z= 0.336
  Chirality :  0.042   0.152   1075
  Planarity :  0.004   0.047   1344
  Dihedral  :  4.571  20.179    995
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.20 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.11 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.28), residues: 904
  helix:  1.58 (0.22), residues: 521
  sheet: -0.89 (0.85), residues: 10
  loop : -0.71 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  95 
 TYR   0.023   0.002   TYR A1085 
 PHE   0.018   0.002   PHE A1118 
 TRP   0.048   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7734)
  covalent geometry    : angle       0.61620 (10395)
  SS BOND              : bond        0.00387 (   14)
  SS BOND              : angle       1.14610 (   28)
  hydrogen bonds       : bond        0.05121 (  431)
  hydrogen bonds       : angle       4.25139 ( 1218)

*********************** 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: 23
    poor density    : 171
  time to evaluate  : 0.184 
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   98 ASN cc_start: 0.8819 (p0) cc_final: 0.8509 (p0)
REVERT: A  167 GLU cc_start: 0.9051 (tp30) cc_final: 0.8696 (mt-10)
REVERT: A  301 TRP cc_start: 0.8866 (m-10) cc_final: 0.8663 (m-10)
REVERT: A  307 ASP cc_start: 0.8468 (m-30) cc_final: 0.8259 (m-30)
REVERT: A  329 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8451 (ptpp)
REVERT: A  387 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7555 (tm-30)
REVERT: A  469 ASP cc_start: 0.8628 (m-30) cc_final: 0.8305 (t0)
REVERT: A  514 LYS cc_start: 0.9163 (tttt) cc_final: 0.8818 (tptm)
REVERT: A  630 MET cc_start: 0.9095 (mmp) cc_final: 0.8849 (mmp)
REVERT: A  638 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7528 (p0)
REVERT: A  673 LYS cc_start: 0.9091 (tttt) cc_final: 0.8875 (tptt)
REVERT: A  762 ARG cc_start: 0.8802 (ttp-110) cc_final: 0.8585 (ttm110)
REVERT: A  883 GLU cc_start: 0.8236 (tt0) cc_final: 0.7639 (pp20)
REVERT: A  894 ARG cc_start: 0.7779 (ptt180) cc_final: 0.7461 (ptt180)
REVERT: A  912 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8110 (ttm110)
REVERT: A  913 TYR cc_start: 0.8810 (m-80) cc_final: 0.8602 (m-10)
REVERT: A  952 MET cc_start: 0.8132 (tpt) cc_final: 0.7822 (tpp)
REVERT: A  963 ASP cc_start: 0.8710 (m-30) cc_final: 0.7575 (t0)
REVERT: A 1032 LYS cc_start: 0.9498 (ttpp) cc_final: 0.9281 (ttpp)
REVERT: A 1072 LYS cc_start: 0.9433 (pttm) cc_final: 0.9177 (pttm)
REVERT: A 1086 LYS cc_start: 0.9641 (mttt) cc_final: 0.9390 (mmmt)
REVERT: A 1126 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8252 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 185
  average time/residue: 0.0879
  time to fit residues: 21.2564
Evaluate side-chains
  169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
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  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  429 LEU
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  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  839 VAL
Chi-restraints excluded: chain A residue 1016 LEU
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 56 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 85 optimal weight:    0.6980
   chunk 89 optimal weight:    7.9990
   chunk 79 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 ASN
A 417 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.107850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.083332 restraints weight = 20474.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.086788 restraints weight = 10986.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.089119 restraints weight = 7431.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.090716 restraints weight = 5751.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.091721 restraints weight = 4822.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.5756

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= 0.145
  Angle     :  0.622   9.492  10423  Z= 0.337
  Chirality :  0.042   0.153   1075
  Planarity :  0.004   0.045   1344
  Dihedral  :  4.577  20.640    995
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.20 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 15.72 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.28), residues: 904
  helix:  1.69 (0.22), residues: 516
  sheet: -0.78 (0.96), residues: 22
  loop : -0.72 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1017 
 TYR   0.024   0.002   TYR A1085 
 PHE   0.014   0.002   PHE A 458 
 TRP   0.057   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7734)
  covalent geometry    : angle       0.62090 (10395)
  SS BOND              : bond        0.00342 (   14)
  SS BOND              : angle       1.04005 (   28)
  hydrogen bonds       : bond        0.04938 (  431)
  hydrogen bonds       : angle       4.28435 ( 1218)

*********************** 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
  199 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 0.316 
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: A   41 GLU cc_start: 0.8871 (pp20) cc_final: 0.8291 (pp20)
REVERT: A   42 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8856 (mmmt)
REVERT: A  167 GLU cc_start: 0.9010 (tp30) cc_final: 0.8683 (mp0)
REVERT: A  227 ASN cc_start: 0.8930 (t0) cc_final: 0.8722 (t0)
REVERT: A  258 PHE cc_start: 0.7805 (m-80) cc_final: 0.7376 (m-80)
REVERT: A  329 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8487 (ptpp)
REVERT: A  469 ASP cc_start: 0.8670 (m-30) cc_final: 0.8331 (t0)
REVERT: A  514 LYS cc_start: 0.9179 (tttt) cc_final: 0.8807 (tptm)
REVERT: A  630 MET cc_start: 0.9173 (mmp) cc_final: 0.8631 (mmp)
REVERT: A  638 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7555 (p0)
REVERT: A  693 GLU cc_start: 0.7546 (pm20) cc_final: 0.6955 (mm-30)
REVERT: A  712 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8625 (t70)
REVERT: A  883 GLU cc_start: 0.8284 (tt0) cc_final: 0.7627 (pp20)
REVERT: A  894 ARG cc_start: 0.7822 (ptt180) cc_final: 0.7492 (ptt180)
REVERT: A  912 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7881 (ttm110)
REVERT: A  952 MET cc_start: 0.8227 (tpt) cc_final: 0.7968 (tpp)
REVERT: A  963 ASP cc_start: 0.8724 (m-30) cc_final: 0.7613 (t0)
REVERT: A 1067 TYR cc_start: 0.9381 (t80) cc_final: 0.9044 (t80)
REVERT: A 1072 LYS cc_start: 0.9399 (pttm) cc_final: 0.9158 (pttm)
REVERT: A 1087 GLU cc_start: 0.9306 (tp30) cc_final: 0.8850 (tp30)
REVERT: A 1130 LYS cc_start: 0.8871 (mttt) cc_final: 0.8507 (tmtt)
  outliers start: 34
  outliers final: 23
  residues processed: 188
  average time/residue: 0.1042
  time to fit residues: 25.5650
Evaluate side-chains
  174 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  466 VAL
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  655 PHE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  712 ASP
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  878 LEU
Chi-restraints excluded: chain A residue 1016 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 91 optimal weight:   20.0000
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 ASN
A 222 ASN
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1070 ASN
A1126 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.107476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.082537 restraints weight = 20700.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.085945 restraints weight = 11290.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.088205 restraints weight = 7718.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.089745 restraints weight = 6027.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.090838 restraints weight = 5110.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.6040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7748  Z= 0.143
  Angle     :  0.620   9.697  10423  Z= 0.334
  Chirality :  0.042   0.161   1075
  Planarity :  0.004   0.043   1344
  Dihedral  :  4.571  20.534    995
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.54 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.26 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.28), residues: 904
  helix:  1.69 (0.22), residues: 513
  sheet: -0.99 (0.93), residues: 22
  loop : -0.84 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 240 
 TYR   0.021   0.002   TYR A 643 
 PHE   0.021   0.002   PHE A 220 
 TRP   0.060   0.002   TRP A 244 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7734)
  covalent geometry    : angle       0.61872 (10395)
  SS BOND              : bond        0.00327 (   14)
  SS BOND              : angle       0.96639 (   28)
  hydrogen bonds       : bond        0.04732 (  431)
  hydrogen bonds       : angle       4.26883 ( 1218)

*********************** 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
  197 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 164
  time to evaluate  : 0.316 
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: 0.8904 (pp20) cc_final: 0.8472 (pp20)
REVERT: A   42 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8821 (mmmt)
REVERT: A   98 ASN cc_start: 0.8880 (p0) cc_final: 0.8600 (p0)
REVERT: A  163 LYS cc_start: 0.4730 (tttt) cc_final: 0.4436 (tttt)
REVERT: A  167 GLU cc_start: 0.9012 (tp30) cc_final: 0.8653 (mp0)
REVERT: A  191 ASP cc_start: 0.9507 (m-30) cc_final: 0.9205 (m-30)
REVERT: A  227 ASN cc_start: 0.9013 (t0) cc_final: 0.8267 (p0)
REVERT: A  329 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8493 (ptpp)
REVERT: A  514 LYS cc_start: 0.9153 (tttt) cc_final: 0.8891 (tttp)
REVERT: A  638 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7608 (p0)
REVERT: A  673 LYS cc_start: 0.9078 (tttt) cc_final: 0.8854 (tptt)
REVERT: A  712 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8626 (t70)
REVERT: A  841 LEU cc_start: 0.9209 (pt) cc_final: 0.8942 (pp)
REVERT: A  883 GLU cc_start: 0.8263 (tt0) cc_final: 0.7841 (tp30)
REVERT: A  894 ARG cc_start: 0.7794 (ptt180) cc_final: 0.7457 (ptt180)
REVERT: A  912 ARG cc_start: 0.8456 (mtt180) cc_final: 0.8060 (ttm110)
REVERT: A  963 ASP cc_start: 0.8729 (m-30) cc_final: 0.7619 (t0)
REVERT: A 1072 LYS cc_start: 0.9376 (pttm) cc_final: 0.9129 (pttm)
REVERT: A 1084 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9195 (mmtt)
REVERT: A 1086 LYS cc_start: 0.9657 (mttt) cc_final: 0.9374 (mmmt)
REVERT: A 1130 LYS cc_start: 0.8920 (mttt) cc_final: 0.8523 (tmtt)
  outliers start: 33
  outliers final: 18
  residues processed: 188
  average time/residue: 0.1074
  time to fit residues: 26.4798
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  : 0.320 
-------------------------------------------------------------------------------
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  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  341 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  655 PHE
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  712 ASP
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 1016 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 66 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 48 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 73 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 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 982 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.105793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.081034 restraints weight = 21149.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.084349 restraints weight = 11794.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.086583 restraints weight = 8161.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.087937 restraints weight = 6408.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.089029 restraints weight = 5498.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.6299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7748  Z= 0.166
  Angle     :  0.654  10.389  10423  Z= 0.351
  Chirality :  0.043   0.183   1075
  Planarity :  0.004   0.043   1344
  Dihedral  :  4.573  21.889    995
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.54 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.71 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.28), residues: 904
  helix:  1.51 (0.22), residues: 523
  sheet: -1.05 (0.97), residues: 20
  loop : -0.95 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 300 
 TYR   0.030   0.002   TYR A 407 
 PHE   0.016   0.002   PHE A 302 
 TRP   0.065   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7734)
  covalent geometry    : angle       0.65327 (10395)
  SS BOND              : bond        0.00312 (   14)
  SS BOND              : angle       0.96269 (   28)
  hydrogen bonds       : bond        0.04726 (  431)
  hydrogen bonds       : angle       4.33118 ( 1218)

*********************** 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: 26
    poor density    : 157
  time to evaluate  : 0.352 
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   41 GLU cc_start: 0.8895 (pp20) cc_final: 0.8323 (pp20)
REVERT: A   42 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8874 (mmmt)
REVERT: A   95 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7339 (ptt90)
REVERT: A   98 ASN cc_start: 0.8879 (p0) cc_final: 0.8601 (p0)
REVERT: A  137 ASP cc_start: 0.8323 (p0) cc_final: 0.7985 (p0)
REVERT: A  163 LYS cc_start: 0.4741 (tttt) cc_final: 0.4359 (mttt)
REVERT: A  167 GLU cc_start: 0.8996 (tp30) cc_final: 0.8636 (mt-10)
REVERT: A  227 ASN cc_start: 0.8987 (t0) cc_final: 0.8738 (t0)
REVERT: A  329 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8477 (ptpp)
REVERT: A  514 LYS cc_start: 0.9073 (tttt) cc_final: 0.8515 (ttmm)
REVERT: A  630 MET cc_start: 0.9063 (mmm) cc_final: 0.8688 (mmm)
REVERT: A  638 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7620 (p0)
REVERT: A  712 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8479 (t70)
REVERT: A  774 LYS cc_start: 0.8911 (mmtm) cc_final: 0.8669 (mmtm)
REVERT: A  841 LEU cc_start: 0.9211 (pt) cc_final: 0.8941 (pp)
REVERT: A  883 GLU cc_start: 0.8232 (tt0) cc_final: 0.7812 (tp30)
REVERT: A  894 ARG cc_start: 0.7792 (ptt180) cc_final: 0.7434 (ptt180)
REVERT: A  912 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8068 (ttm110)
REVERT: A  963 ASP cc_start: 0.8671 (m-30) cc_final: 0.7539 (t0)
REVERT: A 1072 LYS cc_start: 0.9342 (pttm) cc_final: 0.9111 (pttm)
REVERT: A 1084 LYS cc_start: 0.9490 (mmtt) cc_final: 0.9234 (mmtt)
REVERT: A 1086 LYS cc_start: 0.9620 (mttt) cc_final: 0.9338 (mmmt)
REVERT: A 1130 LYS cc_start: 0.8961 (mttt) cc_final: 0.8516 (tmtt)
  outliers start: 26
  outliers final: 18
  residues processed: 176
  average time/residue: 0.1165
  time to fit residues: 26.4878
Evaluate side-chains
  163 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  629 ILE
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  712 ASP
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 1064 CYS
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 55 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0470
   chunk 11 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 66 optimal weight:    0.3980
   chunk 17 optimal weight:    8.9990
   chunk 81 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 80 optimal weight:    0.1980
   chunk 26 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3888 r_free = 0.3888 target = 0.107802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.083295 restraints weight = 20807.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086693 restraints weight = 11486.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.088949 restraints weight = 7860.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.090450 restraints weight = 6132.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.091529 restraints weight = 5200.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.6518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7748  Z= 0.142
  Angle     :  0.684  12.734  10423  Z= 0.364
  Chirality :  0.043   0.247   1075
  Planarity :  0.004   0.057   1344
  Dihedral  :  4.514  21.643    995
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.76 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.16 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.28), residues: 904
  helix:  1.43 (0.22), residues: 520
  sheet: -1.10 (1.29), residues: 12
  loop : -0.98 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 300 
 TYR   0.050   0.002   TYR A1067 
 PHE   0.020   0.002   PHE A 654 
 TRP   0.064   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7734)
  covalent geometry    : angle       0.68348 (10395)
  SS BOND              : bond        0.00295 (   14)
  SS BOND              : angle       0.87252 (   28)
  hydrogen bonds       : bond        0.04694 (  431)
  hydrogen bonds       : angle       4.39482 ( 1218)

*********************** 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
  183 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.301 
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: A   41 GLU cc_start: 0.8877 (pp20) cc_final: 0.8283 (pp20)
REVERT: A   42 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8868 (mmmt)
REVERT: A   95 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7332 (ptt90)
REVERT: A   97 MET cc_start: 0.8554 (tpp) cc_final: 0.8138 (mmm)
REVERT: A   98 ASN cc_start: 0.8853 (p0) cc_final: 0.8589 (p0)
REVERT: A  137 ASP cc_start: 0.8305 (p0) cc_final: 0.8034 (p0)
REVERT: A  163 LYS cc_start: 0.4767 (tttt) cc_final: 0.4496 (tttt)
REVERT: A  167 GLU cc_start: 0.8983 (tp30) cc_final: 0.8648 (mt-10)
REVERT: A  227 ASN cc_start: 0.8964 (t0) cc_final: 0.8671 (t0)
REVERT: A  329 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8476 (ptpp)
REVERT: A  514 LYS cc_start: 0.9209 (tttt) cc_final: 0.8786 (tttp)
REVERT: A  515 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7493 (mm-30)
REVERT: A  651 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7383 (p90)
REVERT: A  712 ASP cc_start: 0.9181 (OUTLIER) cc_final: 0.8651 (t70)
REVERT: A  774 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8672 (mmtm)
REVERT: A  841 LEU cc_start: 0.9171 (pt) cc_final: 0.8898 (pp)
REVERT: A  883 GLU cc_start: 0.8182 (tt0) cc_final: 0.7748 (tp30)
REVERT: A  912 ARG cc_start: 0.8468 (mtt180) cc_final: 0.8049 (ttm110)
REVERT: A  963 ASP cc_start: 0.8683 (m-30) cc_final: 0.7548 (t0)
REVERT: A  975 ARG cc_start: 0.8627 (mtm180) cc_final: 0.8333 (mtm180)
REVERT: A 1067 TYR cc_start: 0.9510 (t80) cc_final: 0.9279 (t80)
REVERT: A 1072 LYS cc_start: 0.9319 (pttm) cc_final: 0.9076 (pttm)
REVERT: A 1130 LYS cc_start: 0.8929 (mttt) cc_final: 0.8487 (tmtt)
  outliers start: 24
  outliers final: 17
  residues processed: 177
  average time/residue: 0.1200
  time to fit residues: 27.4119
Evaluate side-chains
  160 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
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  712 ASP
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 1016 LEU
Chi-restraints excluded: chain A residue 1095 TYR
Chi-restraints excluded: chain A residue 1117 ASP
Chi-restraints excluded: chain A residue 1126 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:   20.0000
   chunk 43 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 507 ASN
A 621 GLN
A 637 HIS
** A 648 ASN ** 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 = 0.3862 r_free = 0.3862 target = 0.106234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.081484 restraints weight = 21112.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.084715 restraints weight = 11690.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.086964 restraints weight = 8103.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.088437 restraints weight = 6357.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.089370 restraints weight = 5410.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.6656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7748  Z= 0.166
  Angle     :  0.707  10.932  10423  Z= 0.381
  Chirality :  0.044   0.210   1075
  Planarity :  0.004   0.042   1344
  Dihedral  :  4.484  21.513    995
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.87 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.56 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.28), residues: 904
  helix:  1.47 (0.22), residues: 518
  sheet: -1.14 (1.12), residues: 12
  loop : -0.95 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 300 
 TYR   0.042   0.002   TYR A1067 
 PHE   0.018   0.002   PHE A 654 
 TRP   0.063   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7734)
  covalent geometry    : angle       0.70698 (10395)
  SS BOND              : bond        0.00305 (   14)
  SS BOND              : angle       0.86698 (   28)
  hydrogen bonds       : bond        0.04776 (  431)
  hydrogen bonds       : angle       4.44399 ( 1218)

*********************** 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: 25
    poor density    : 146
  time to evaluate  : 0.303 
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   41 GLU cc_start: 0.8887 (pp20) cc_final: 0.8436 (pp20)
REVERT: A   42 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8793 (mmmt)
REVERT: A   95 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7432 (ptt90)
REVERT: A   97 MET cc_start: 0.8554 (tpp) cc_final: 0.8139 (mmm)
REVERT: A   98 ASN cc_start: 0.8854 (p0) cc_final: 0.8577 (p0)
REVERT: A  137 ASP cc_start: 0.8319 (p0) cc_final: 0.8054 (p0)
REVERT: A  163 LYS cc_start: 0.4869 (tttt) cc_final: 0.4295 (tttt)
REVERT: A  167 GLU cc_start: 0.8993 (tp30) cc_final: 0.8658 (mt-10)
REVERT: A  227 ASN cc_start: 0.8960 (t0) cc_final: 0.8670 (t0)
REVERT: A  329 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8487 (ptpp)
REVERT: A  514 LYS cc_start: 0.9232 (tttt) cc_final: 0.8596 (tttp)
REVERT: A  515 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7447 (mm-30)
REVERT: A  630 MET cc_start: 0.9052 (mmm) cc_final: 0.8769 (mmm)
REVERT: A  712 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8381 (t70)
REVERT: A  883 GLU cc_start: 0.8156 (tt0) cc_final: 0.7722 (tp30)
REVERT: A  894 ARG cc_start: 0.7655 (ptt90) cc_final: 0.7175 (tmm-80)
REVERT: A  912 ARG cc_start: 0.8550 (mtt180) cc_final: 0.8133 (ttm110)
REVERT: A  963 ASP cc_start: 0.8660 (m-30) cc_final: 0.7535 (t0)
REVERT: A  975 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8347 (mtm180)
REVERT: A 1072 LYS cc_start: 0.9320 (pttm) cc_final: 0.9070 (pttm)
REVERT: A 1130 LYS cc_start: 0.8917 (mttt) cc_final: 0.8482 (tmtt)
  outliers start: 25
  outliers final: 18
  residues processed: 163
  average time/residue: 0.1033
  time to fit residues: 21.7868
Evaluate side-chains
  156 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
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  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  507 ASN
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  712 ASP
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 1016 LEU
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 1 optimal weight:    0.0870
   chunk 62 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 71 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.0760

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.106462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.081521 restraints weight = 21185.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.084776 restraints weight = 11845.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.086964 restraints weight = 8219.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.088449 restraints weight = 6484.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.089471 restraints weight = 5524.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.6768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7748  Z= 0.166
  Angle     :  0.724  12.002  10423  Z= 0.391
  Chirality :  0.044   0.206   1075
  Planarity :  0.005   0.108   1344
  Dihedral  :  4.684  30.501    995
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.98 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.68 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.28), residues: 904
  helix:  1.39 (0.22), residues: 518
  sheet: -1.16 (1.00), residues: 12
  loop : -0.98 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 300 
 TYR   0.032   0.002   TYR A1067 
 PHE   0.016   0.002   PHE A 654 
 TRP   0.069   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7734)
  covalent geometry    : angle       0.72323 (10395)
  SS BOND              : bond        0.00301 (   14)
  SS BOND              : angle       0.86490 (   28)
  hydrogen bonds       : bond        0.04845 (  431)
  hydrogen bonds       : angle       4.49883 ( 1218)

********************** 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
  165 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.256 
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   41 GLU cc_start: 0.8889 (pp20) cc_final: 0.8451 (pp20)
REVERT: A   42 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8785 (mmmt)
REVERT: A   95 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7420 (ptt90)
REVERT: A   97 MET cc_start: 0.8586 (tpp) cc_final: 0.8252 (mmm)
REVERT: A  137 ASP cc_start: 0.8333 (p0) cc_final: 0.8074 (p0)
REVERT: A  163 LYS cc_start: 0.4896 (tttt) cc_final: 0.4438 (mttt)
REVERT: A  167 GLU cc_start: 0.8994 (tp30) cc_final: 0.8707 (mt-10)
REVERT: A  227 ASN cc_start: 0.8961 (t0) cc_final: 0.8689 (t0)
REVERT: A  329 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8489 (ptpp)
REVERT: A  514 LYS cc_start: 0.9261 (tttt) cc_final: 0.8628 (tttp)
REVERT: A  515 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7501 (mm-30)
REVERT: A  630 MET cc_start: 0.9037 (mmm) cc_final: 0.8756 (mmm)
REVERT: A  651 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7402 (p90)
REVERT: A  659 ILE cc_start: 0.8694 (mm) cc_final: 0.8374 (tp)
REVERT: A  693 GLU cc_start: 0.7722 (pm20) cc_final: 0.7418 (pm20)
REVERT: A  712 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8480 (t70)
REVERT: A  883 GLU cc_start: 0.8056 (tt0) cc_final: 0.7647 (tp30)
REVERT: A  894 ARG cc_start: 0.7645 (ptt90) cc_final: 0.7183 (tmm-80)
REVERT: A  912 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8098 (ttm110)
REVERT: A  963 ASP cc_start: 0.8676 (m-30) cc_final: 0.7521 (t0)
REVERT: A  975 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8344 (mtm180)
REVERT: A 1072 LYS cc_start: 0.9310 (pttm) cc_final: 0.9048 (pttm)
REVERT: A 1130 LYS cc_start: 0.8899 (mttt) cc_final: 0.8463 (tmtt)
  outliers start: 23
  outliers final: 16
  residues processed: 157
  average time/residue: 0.0970
  time to fit residues: 19.8629
Evaluate side-chains
  155 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
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  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  712 ASP
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 1016 LEU
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 25 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0870
   chunk 35 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.9562

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

Flipped N/Q/H residues before XYZ refinement:
A 175 ASN
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 621 GLN
** A 648 ASN ** 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 = 0.3885 r_free = 0.3885 target = 0.107119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.082299 restraints weight = 20971.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.085664 restraints weight = 11389.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.087991 restraints weight = 7787.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.089477 restraints weight = 6068.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.090523 restraints weight = 5157.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.6908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7748  Z= 0.158
  Angle     :  0.726  12.256  10423  Z= 0.392
  Chirality :  0.044   0.209   1075
  Planarity :  0.005   0.139   1344
  Dihedral  :  4.690  35.770    995
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.09 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 21.64 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.28), residues: 904
  helix:  1.42 (0.22), residues: 517
  sheet: -0.77 (1.04), residues: 12
  loop : -1.01 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 300 
 TYR   0.035   0.002   TYR A1067 
 PHE   0.015   0.002   PHE A 458 
 TRP   0.066   0.002   TRP A 244 
 HIS   0.002   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7734)
  covalent geometry    : angle       0.72596 (10395)
  SS BOND              : bond        0.00301 (   14)
  SS BOND              : angle       0.84912 (   28)
  hydrogen bonds       : bond        0.04801 (  431)
  hydrogen bonds       : angle       4.47204 ( 1218)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1680.12 seconds
wall clock time: 29 minutes 51.82 seconds (1791.82 seconds total)