Starting phenix.real_space_refine
on Wed Mar 12 08:45:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c3y_16415/03_2025/8c3y_16415.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c3y_16415/03_2025/8c3y_16415.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c3y_16415/03_2025/8c3y_16415.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c3y_16415/03_2025/8c3y_16415.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c3y_16415/03_2025/8c3y_16415.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c3y_16415/03_2025/8c3y_16415.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7580
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 929, 7580
          Classifications: {'peptide': 929}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 903}
          Chain breaks: 12
  Time building chain proxies: 4.78, per 1000 atoms: 0.63
  Number of scatterers: 7580
  At special positions: 0
  Unit cell: (74.88, 117.312, 107.328, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1441      8.00
     N    1319      7.00
     C    4777      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 109 " - pdb=" SG  CYS A 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 182 " - pdb=" SG  CYS A 281 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 310 " - pdb=" SG  CYS A 435 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 324 " - pdb=" SG  CYS A 359 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 356 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 340 " - pdb=" SG  CYS A 467 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 464 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 526 " - pdb=" SG  CYS A 614 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 542 " - pdb=" SG  CYS A 553 " distance=2.09
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 608 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 605 " - pdb=" SG  CYS A 719 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 612 " - pdb=" SG  CYS A 710 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 908 " - pdb=" SG  CYS A1000 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 951.0 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 3 sheets defined
      61.7% alpha, 2.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 42
      removed outlier: 3.853A  pdb=" N   LYS A  30 " --> pdb=" O   GLU A  26 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ASP A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ILE A  32 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 97
      removed outlier: 3.966A  pdb=" N   ARG A  95 " --> pdb=" O   PRO A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 134
    Processing helix  chain 'A' and resid 137 through 142
    Processing helix  chain 'A' and resid 150 through 172
    Processing helix  chain 'A' and resid 179 through 197
    Processing helix  chain 'A' and resid 212 through 227
    Processing helix  chain 'A' and resid 227 through 232
      removed outlier: 4.131A  pdb=" N   LEU A 231 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 256
      removed outlier: 5.536A  pdb=" N   GLU A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ASP A 250 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 324
    Processing helix  chain 'A' and resid 327 through 330
    Processing helix  chain 'A' and resid 356 through 393
      Proline residue:  A 365  - end of helix
    Processing helix  chain 'A' and resid 413 through 418
    Processing helix  chain 'A' and resid 421 through 431
      removed outlier: 4.190A  pdb=" N   GLU A 431 " --> pdb=" O   LYS A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 523
    Processing helix  chain 'A' and resid 523 through 528
    Processing helix  chain 'A' and resid 571 through 593
    Processing helix  chain 'A' and resid 593 through 598
    Processing helix  chain 'A' and resid 604 through 631
      removed outlier: 4.150A  pdb=" N   CYS A 608 " --> pdb=" O   ASP A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 644
    Processing helix  chain 'A' and resid 648 through 654
      removed outlier: 3.570A  pdb=" N   ASP A 652 " --> pdb=" O   ASP A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 659
    Processing helix  chain 'A' and resid 666 through 686
    Processing helix  chain 'A' and resid 690 through 713
      removed outlier: 3.932A  pdb=" N   ALA A 694 " --> pdb=" O   LYS A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 719
      removed outlier: 6.422A  pdb=" N   GLU A 717 " --> pdb=" O   ASN A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 763
    Processing helix  chain 'A' and resid 764 through 769
    Processing helix  chain 'A' and resid 844 through 848
    Processing helix  chain 'A' and resid 869 through 892
    Processing helix  chain 'A' and resid 904 through 924
    Processing helix  chain 'A' and resid 931 through 952
    Processing helix  chain 'A' and resid 954 through 962
      removed outlier: 3.882A  pdb=" N   ASN A 958 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   GLN A 959 " --> pdb=" O   LYS A 956 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   LYS A 960 " --> pdb=" O   ASP A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 967
    Processing helix  chain 'A' and resid 971 through 994
      removed outlier: 5.401A  pdb=" N   ASP A 984 " --> pdb=" O   GLU A 980 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   GLN A 985 " --> pdb=" O   ALA A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1040
    Processing helix  chain 'A' and resid 1058 through 1097
    Processing helix  chain 'A' and resid 1113 through 1126
    Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 267
    Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 326
    Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 509
      removed outlier: 7.006A  pdb=" N   GLN A 539 " --> pdb=" O   GLU A 556 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS A 552 " --> pdb=" O   TYR A 543 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1218 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 2.09 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.610
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.870
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.830
-------------------------------------------------------------------------------
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   7734  Z= 1.150
  Angle     :  1.562   8.860  10395  Z= 1.101
  Chirality :  0.097   0.479   1075
  Planarity :  0.010   0.166   1344
  Dihedral  : 10.954  89.353   2920
  Min Nonbonded Distance : 2.226

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

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

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

*********************** 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  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 LYS cc_start: 0.5720 (mttt) cc_final: 0.5253 (tttm)
REVERT: A  170 VAL cc_start: 0.7961 (m) cc_final: 0.7739 (m)
REVERT: A  256 THR cc_start: 0.8987 (p) cc_final: 0.8710 (t)
REVERT: A  291 ASN cc_start: 0.8715 (m-40) cc_final: 0.8486 (m-40)
REVERT: A  514 LYS cc_start: 0.8747 (tttt) cc_final: 0.8189 (tptm)
REVERT: A  647 ILE cc_start: 0.8356 (mt) cc_final: 0.8134 (mt)
REVERT: A  883 GLU cc_start: 0.8457 (tt0) cc_final: 0.8059 (pp20)
REVERT: A  912 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8578 (ttm110)
REVERT: A  991 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8450 (ttmt)
REVERT: A 1067 TYR cc_start: 0.9453 (t80) cc_final: 0.9000 (t80)
REVERT: A 1084 LYS cc_start: 0.9275 (mttt) cc_final: 0.9064 (mmtt)
  outliers start: 4
  outliers final: 0
  residues processed: 298
  average time/residue: 0.2696
  time to fit residues: 100.3747
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  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 9

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7734  Z= 0.265
  Angle     :  0.738   9.366  10395  Z= 0.415
  Chirality :  0.045   0.185   1075
  Planarity :  0.005   0.059   1344
  Dihedral  :  4.845  20.574    995
  Min Nonbonded Distance : 2.299

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

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

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

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

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 194
  time to evaluate  : 1.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 GLU cc_start: 0.9176 (tp30) cc_final: 0.8889 (tp30)
REVERT: A  180 GLU cc_start: 0.8487 (tt0) cc_final: 0.7830 (tt0)
REVERT: A  243 TRP cc_start: 0.9087 (t60) cc_final: 0.8847 (t60)
REVERT: A  258 PHE cc_start: 0.8059 (m-80) cc_final: 0.7591 (m-80)
REVERT: A  307 ASP cc_start: 0.8660 (m-30) cc_final: 0.8360 (m-30)
REVERT: A  469 ASP cc_start: 0.8649 (m-30) cc_final: 0.8379 (t0)
REVERT: A  514 LYS cc_start: 0.9075 (tttt) cc_final: 0.8823 (tptm)
REVERT: A  555 MET cc_start: 0.6998 (mtp) cc_final: 0.6675 (mtp)
REVERT: A  595 TYR cc_start: 0.7830 (t80) cc_final: 0.7527 (t80)
REVERT: A  883 GLU cc_start: 0.8413 (tt0) cc_final: 0.7812 (pp20)
REVERT: A  912 ARG cc_start: 0.8518 (mtt180) cc_final: 0.7948 (ttm110)
REVERT: A  952 MET cc_start: 0.8304 (tpt) cc_final: 0.8039 (tpp)
  outliers start: 24
  outliers final: 16
  residues processed: 208
  average time/residue: 0.2405
  time to fit residues: 64.3435
Evaluate side-chains
  169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1098 ASN
Chi-restraints excluded: chain A residue 1117 ASP
Chi-restraints excluded: chain A residue 1126 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 12 optimal weight:    0.0060
   chunk 48 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8798

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

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

Total number of N/Q/H flips: 2

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7734  Z= 0.222
  Angle     :  0.676   9.381  10395  Z= 0.368
  Chirality :  0.044   0.162   1075
  Planarity :  0.005   0.051   1344
  Dihedral  :  4.773  22.160    995
  Min Nonbonded Distance : 2.397

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

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

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

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

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 175
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 LYS cc_start: 0.9335 (mmmt) cc_final: 0.8567 (mmmt)
REVERT: A  137 ASP cc_start: 0.8537 (p0) cc_final: 0.8330 (p0)
REVERT: A  167 GLU cc_start: 0.9058 (tp30) cc_final: 0.8641 (mp0)
REVERT: A  180 GLU cc_start: 0.8595 (tt0) cc_final: 0.8258 (tt0)
REVERT: A  194 ASP cc_start: 0.9185 (m-30) cc_final: 0.8492 (m-30)
REVERT: A  260 ASP cc_start: 0.5593 (t70) cc_final: 0.5291 (t70)
REVERT: A  307 ASP cc_start: 0.8679 (m-30) cc_final: 0.8468 (m-30)
REVERT: A  469 ASP cc_start: 0.8809 (m-30) cc_final: 0.8496 (t0)
REVERT: A  514 LYS cc_start: 0.9223 (tttt) cc_final: 0.8852 (tptm)
REVERT: A  555 MET cc_start: 0.7541 (mtp) cc_final: 0.7180 (mtp)
REVERT: A  638 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7567 (p0)
REVERT: A  883 GLU cc_start: 0.8382 (tt0) cc_final: 0.7707 (pp20)
REVERT: A  912 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7824 (ttm110)
REVERT: A  913 TYR cc_start: 0.8930 (m-80) cc_final: 0.8488 (m-10)
REVERT: A  917 ASP cc_start: 0.9146 (m-30) cc_final: 0.8843 (m-30)
REVERT: A  952 MET cc_start: 0.8422 (tpt) cc_final: 0.8167 (tpp)
REVERT: A  963 ASP cc_start: 0.8748 (m-30) cc_final: 0.7629 (t0)
REVERT: A 1014 GLN cc_start: 0.8350 (tt0) cc_final: 0.7147 (mm-40)
REVERT: A 1018 TRP cc_start: 0.9136 (m-10) cc_final: 0.8430 (m100)
REVERT: A 1072 LYS cc_start: 0.9421 (pttm) cc_final: 0.9183 (pttm)
  outliers start: 35
  outliers final: 21
  residues processed: 195
  average time/residue: 0.2127
  time to fit residues: 54.6814
Evaluate side-chains
  171 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1064 CYS
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 ASP
Chi-restraints excluded: chain A residue 1126 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 91 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 134 HIS
A 175 ASN
A 393 HIS
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.107459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.082994 restraints weight = 20728.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.086453 restraints weight = 10890.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.088854 restraints weight = 7347.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.5442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7734  Z= 0.232
  Angle     :  0.634   8.824  10395  Z= 0.350
  Chirality :  0.043   0.159   1075
  Planarity :  0.005   0.079   1344
  Dihedral  :  4.618  20.114    995
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.98 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 14.63 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.28), residues: 904
  helix:  1.52 (0.21), residues: 519
  sheet: -0.03 (1.03), residues: 22
  loop : -0.64 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A 134 
 PHE   0.018   0.002   PHE A1118 
 TYR   0.028   0.002   TYR A1067 
 ARG   0.006   0.001   ARG A1017 

*********************** 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
  196 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 0.856 
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   41 GLU cc_start: 0.8858 (pp20) cc_final: 0.8342 (pp20)
REVERT: A  167 GLU cc_start: 0.9010 (tp30) cc_final: 0.8707 (mp0)
REVERT: A  180 GLU cc_start: 0.8568 (tt0) cc_final: 0.8231 (tt0)
REVERT: A  307 ASP cc_start: 0.8452 (m-30) cc_final: 0.8244 (m-30)
REVERT: A  423 ASN cc_start: 0.9187 (m-40) cc_final: 0.8964 (p0)
REVERT: A  514 LYS cc_start: 0.9162 (tttt) cc_final: 0.8805 (tptm)
REVERT: A  625 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6160 (mp0)
REVERT: A  638 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7577 (p0)
REVERT: A  758 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8848 (tt0)
REVERT: A  883 GLU cc_start: 0.8318 (tt0) cc_final: 0.7679 (pp20)
REVERT: A  912 ARG cc_start: 0.8577 (mtt180) cc_final: 0.8183 (ttm110)
REVERT: A  913 TYR cc_start: 0.8898 (m-80) cc_final: 0.8504 (m-10)
REVERT: A  917 ASP cc_start: 0.8967 (m-30) cc_final: 0.8539 (m-30)
REVERT: A  952 MET cc_start: 0.8248 (tpt) cc_final: 0.7922 (tpp)
REVERT: A  963 ASP cc_start: 0.8749 (m-30) cc_final: 0.7647 (t0)
REVERT: A 1014 GLN cc_start: 0.8489 (tt0) cc_final: 0.7346 (mm-40)
REVERT: A 1018 TRP cc_start: 0.9120 (m-10) cc_final: 0.8453 (m-10)
REVERT: A 1072 LYS cc_start: 0.9421 (pttm) cc_final: 0.9140 (pttm)
REVERT: A 1126 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8392 (t0)
  outliers start: 33
  outliers final: 20
  residues processed: 183
  average time/residue: 0.2207
  time to fit residues: 53.0849
Evaluate side-chains
  171 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  758 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 ASP
Chi-restraints excluded: chain A residue 1126 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0670
   chunk 90 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7118

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.107314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.082877 restraints weight = 20360.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.086254 restraints weight = 11170.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.088503 restraints weight = 7631.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.5822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7734  Z= 0.192
  Angle     :  0.621   8.964  10395  Z= 0.335
  Chirality :  0.042   0.160   1075
  Planarity :  0.004   0.050   1344
  Dihedral  :  4.597  21.192    995
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.42 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 15.48 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.28), residues: 904
  helix:  1.59 (0.22), residues: 514
  sheet: -0.06 (1.02), residues: 24
  loop : -0.75 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 
 PHE   0.015   0.002   PHE A 220 
 TYR   0.024   0.002   TYR A1067 
 ARG   0.008   0.001   ARG A 300 

*********************** 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
  195 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 161
  time to evaluate  : 0.914 
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   98 ASN cc_start: 0.8929 (p0) cc_final: 0.8666 (p0)
REVERT: A  167 GLU cc_start: 0.8967 (tp30) cc_final: 0.8635 (mp0)
REVERT: A  180 GLU cc_start: 0.8530 (tt0) cc_final: 0.8214 (tt0)
REVERT: A  194 ASP cc_start: 0.9200 (m-30) cc_final: 0.8710 (m-30)
REVERT: A  258 PHE cc_start: 0.7627 (m-80) cc_final: 0.7405 (m-80)
REVERT: A  514 LYS cc_start: 0.9178 (tttt) cc_final: 0.8946 (tttp)
REVERT: A  625 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5861 (mp0)
REVERT: A  630 MET cc_start: 0.9008 (mmp) cc_final: 0.8746 (mmp)
REVERT: A  673 LYS cc_start: 0.9107 (tttt) cc_final: 0.8845 (tptt)
REVERT: A  883 GLU cc_start: 0.8326 (tt0) cc_final: 0.7649 (pp20)
REVERT: A  912 ARG cc_start: 0.8531 (mtt180) cc_final: 0.8117 (ttm110)
REVERT: A  913 TYR cc_start: 0.8900 (m-80) cc_final: 0.8520 (m-10)
REVERT: A  917 ASP cc_start: 0.9102 (m-30) cc_final: 0.8684 (m-30)
REVERT: A  952 MET cc_start: 0.8373 (tpt) cc_final: 0.8122 (tpp)
REVERT: A  963 ASP cc_start: 0.8763 (m-30) cc_final: 0.7643 (t0)
REVERT: A  980 GLU cc_start: 0.8671 (tp30) cc_final: 0.8461 (tp30)
REVERT: A  982 ASN cc_start: 0.8869 (m-40) cc_final: 0.8666 (m110)
REVERT: A 1014 GLN cc_start: 0.8380 (tt0) cc_final: 0.7233 (mm-40)
REVERT: A 1018 TRP cc_start: 0.9086 (m-10) cc_final: 0.8439 (m-10)
REVERT: A 1037 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9074 (mm)
REVERT: A 1072 LYS cc_start: 0.9412 (pttm) cc_final: 0.9153 (pttm)
REVERT: A 1130 LYS cc_start: 0.8889 (mttt) cc_final: 0.8490 (tmtt)
  outliers start: 34
  outliers final: 22
  residues processed: 185
  average time/residue: 0.2108
  time to fit residues: 51.8169
Evaluate side-chains
  167 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  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  878 LEU
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1064 CYS
Chi-restraints excluded: chain A residue 1095 TYR
Chi-restraints excluded: chain A residue 1117 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 12 optimal weight:    0.0040
   chunk 41 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 16 optimal weight:   20.0000
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   overall best weight:    1.6000

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

Flipped N/Q/H residues before XYZ refinement:
A 175 ASN
A 417 ASN
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1126 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.104653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.080285 restraints weight = 20701.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.083490 restraints weight = 11507.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.085611 restraints weight = 7947.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.6124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7734  Z= 0.258
  Angle     :  0.642  10.211  10395  Z= 0.350
  Chirality :  0.042   0.152   1075
  Planarity :  0.004   0.039   1344
  Dihedral  :  4.586  19.377    995
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.65 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 17.65 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.28), residues: 904
  helix:  1.55 (0.22), residues: 519
  sheet: -0.42 (0.96), residues: 24
  loop : -0.82 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A 756 
 PHE   0.018   0.002   PHE A 651 
 TYR   0.023   0.002   TYR A 643 
 ARG   0.007   0.001   ARG A 300 

*********************** 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
  190 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 152
  time to evaluate  : 0.869 
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  167 GLU cc_start: 0.8966 (tp30) cc_final: 0.8693 (mp0)
REVERT: A  180 GLU cc_start: 0.8563 (tt0) cc_final: 0.8275 (tt0)
REVERT: A  194 ASP cc_start: 0.9164 (m-30) cc_final: 0.8664 (m-30)
REVERT: A  307 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8048 (t0)
REVERT: A  514 LYS cc_start: 0.9131 (tttt) cc_final: 0.8445 (ttmm)
REVERT: A  625 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.5840 (mp0)
REVERT: A  630 MET cc_start: 0.9049 (mmp) cc_final: 0.8818 (mmp)
REVERT: A  638 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.7725 (p0)
REVERT: A  693 GLU cc_start: 0.7841 (pm20) cc_final: 0.7555 (pm20)
REVERT: A  758 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8883 (tt0)
REVERT: A  774 LYS cc_start: 0.8936 (mmtm) cc_final: 0.8700 (mmtm)
REVERT: A  883 GLU cc_start: 0.8318 (tt0) cc_final: 0.7643 (pp20)
REVERT: A  894 ARG cc_start: 0.7649 (ptt90) cc_final: 0.7125 (tmm-80)
REVERT: A  913 TYR cc_start: 0.8940 (m-80) cc_final: 0.8541 (m-10)
REVERT: A  952 MET cc_start: 0.8296 (tpt) cc_final: 0.8026 (tpp)
REVERT: A  963 ASP cc_start: 0.8699 (m-30) cc_final: 0.7546 (t0)
REVERT: A  975 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8494 (mtm180)
REVERT: A  982 ASN cc_start: 0.8996 (m-40) cc_final: 0.8759 (m110)
REVERT: A 1037 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8802 (mm)
REVERT: A 1067 TYR cc_start: 0.9432 (t80) cc_final: 0.9125 (t80)
REVERT: A 1072 LYS cc_start: 0.9390 (pttm) cc_final: 0.9121 (pttm)
REVERT: A 1130 LYS cc_start: 0.8948 (mttt) cc_final: 0.8505 (tmtt)
  outliers start: 38
  outliers final: 23
  residues processed: 178
  average time/residue: 0.2014
  time to fit residues: 48.1388
Evaluate side-chains
  165 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  758 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1037 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0970
   chunk 80 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0670
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 749 GLN ** 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 = 0.3884 r_free = 0.3884 target = 0.107622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.083082 restraints weight = 20644.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.086495 restraints weight = 11470.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.088725 restraints weight = 7871.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.6401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7734  Z= 0.186
  Angle     :  0.631  10.112  10395  Z= 0.342
  Chirality :  0.042   0.155   1075
  Planarity :  0.004   0.036   1344
  Dihedral  :  4.530  20.303    995
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.54 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 19.71 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.28), residues: 904
  helix:  1.64 (0.22), residues: 516
  sheet: -0.45 (0.90), residues: 22
  loop : -0.84 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 
 PHE   0.021   0.002   PHE A 654 
 TYR   0.023   0.002   TYR A 544 
 ARG   0.006   0.001   ARG A 300 

*********************** 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
  184 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ASN cc_start: 0.8896 (p0) cc_final: 0.8688 (p0)
REVERT: A  167 GLU cc_start: 0.8959 (tp30) cc_final: 0.8633 (mp0)
REVERT: A  180 GLU cc_start: 0.8513 (tt0) cc_final: 0.8125 (mt-10)
REVERT: A  194 ASP cc_start: 0.8988 (m-30) cc_final: 0.8481 (m-30)
REVERT: A  307 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8015 (t0)
REVERT: A  514 LYS cc_start: 0.9196 (tttt) cc_final: 0.8574 (tttp)
REVERT: A  515 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7599 (mm-30)
REVERT: A  625 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.5761 (mp0)
REVERT: A  630 MET cc_start: 0.9062 (mmp) cc_final: 0.8756 (mmp)
REVERT: A  638 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7676 (p0)
REVERT: A  883 GLU cc_start: 0.8269 (tt0) cc_final: 0.7572 (pp20)
REVERT: A  894 ARG cc_start: 0.7610 (ptt90) cc_final: 0.7120 (tmm-80)
REVERT: A  912 ARG cc_start: 0.8426 (mtt180) cc_final: 0.7850 (ttm110)
REVERT: A  952 MET cc_start: 0.8264 (tpt) cc_final: 0.8028 (tpp)
REVERT: A  963 ASP cc_start: 0.8729 (m-30) cc_final: 0.7580 (t0)
REVERT: A  975 ARG cc_start: 0.8683 (mtm180) cc_final: 0.8399 (mtm180)
REVERT: A  982 ASN cc_start: 0.8925 (m-40) cc_final: 0.8638 (m110)
REVERT: A 1017 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7895 (mtm180)
REVERT: A 1067 TYR cc_start: 0.9416 (t80) cc_final: 0.9197 (t80)
REVERT: A 1072 LYS cc_start: 0.9320 (pttm) cc_final: 0.9066 (pttm)
REVERT: A 1084 LYS cc_start: 0.9443 (mmtt) cc_final: 0.9130 (mmtt)
REVERT: A 1130 LYS cc_start: 0.8922 (mttt) cc_final: 0.8484 (tmtt)
  outliers start: 29
  outliers final: 20
  residues processed: 174
  average time/residue: 0.2098
  time to fit residues: 48.0802
Evaluate side-chains
  172 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  638 ASP
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  655 PHE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1095 TYR
Chi-restraints excluded: chain A residue 1117 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0060
   chunk 67 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   overall best weight:    1.9400

-------------------------------------------------------------------------------
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 637 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.103634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.078898 restraints weight = 21645.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.082044 restraints weight = 12196.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.084180 restraints weight = 8549.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.6634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7734  Z= 0.295
  Angle     :  0.670  10.588  10395  Z= 0.369
  Chirality :  0.044   0.204   1075
  Planarity :  0.004   0.037   1344
  Dihedral  :  4.590  24.647    995
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.31 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 19.83 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.28), residues: 904
  helix:  1.48 (0.22), residues: 517
  sheet: -0.21 (0.96), residues: 24
  loop : -0.93 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.003   TRP A 244 
 HIS   0.004   0.001   HIS A 702 
 PHE   0.020   0.003   PHE A 571 
 TYR   0.024   0.002   TYR A 643 
 ARG   0.006   0.001   ARG A 300 

*********************** 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
  178 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 149
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ASN cc_start: 0.8941 (p0) cc_final: 0.8705 (p0)
REVERT: A  167 GLU cc_start: 0.9003 (tp30) cc_final: 0.8653 (mt-10)
REVERT: A  180 GLU cc_start: 0.8654 (tt0) cc_final: 0.8375 (tt0)
REVERT: A  194 ASP cc_start: 0.8948 (m-30) cc_final: 0.8483 (m-30)
REVERT: A  227 ASN cc_start: 0.8956 (t0) cc_final: 0.8679 (t0)
REVERT: A  514 LYS cc_start: 0.9314 (tttt) cc_final: 0.8673 (tttp)
REVERT: A  515 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7744 (mm-30)
REVERT: A  625 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5885 (mp0)
REVERT: A  630 MET cc_start: 0.9162 (mmp) cc_final: 0.8891 (mmp)
REVERT: A  651 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7512 (p90)
REVERT: A  673 LYS cc_start: 0.9127 (tttt) cc_final: 0.8882 (tmtt)
REVERT: A  758 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8902 (tt0)
REVERT: A  774 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8728 (mmtm)
REVERT: A  883 GLU cc_start: 0.8330 (tt0) cc_final: 0.7628 (pp20)
REVERT: A  894 ARG cc_start: 0.7666 (ptt90) cc_final: 0.7187 (tmm-80)
REVERT: A  975 ARG cc_start: 0.8687 (mtm180) cc_final: 0.8195 (mtm-85)
REVERT: A  982 ASN cc_start: 0.9047 (m-40) cc_final: 0.8752 (m110)
REVERT: A 1014 GLN cc_start: 0.8429 (tt0) cc_final: 0.8201 (tt0)
REVERT: A 1017 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8262 (mtm180)
REVERT: A 1067 TYR cc_start: 0.9455 (t80) cc_final: 0.9207 (t80)
REVERT: A 1072 LYS cc_start: 0.9324 (pttm) cc_final: 0.9072 (pttm)
REVERT: A 1084 LYS cc_start: 0.9456 (mmtt) cc_final: 0.9167 (mmtt)
REVERT: A 1130 LYS cc_start: 0.8941 (mttt) cc_final: 0.8461 (tmtt)
  outliers start: 29
  outliers final: 22
  residues processed: 167
  average time/residue: 0.2154
  time to fit residues: 48.1120
Evaluate side-chains
  165 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  651 PHE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  758 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  926 ASP
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1095 TYR
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 89 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0570
   chunk 91 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 35 optimal weight:    0.5980
   chunk 83 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.6898

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.106031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.081496 restraints weight = 21130.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.084850 restraints weight = 11682.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.087076 restraints weight = 8039.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.6763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7734  Z= 0.197
  Angle     :  0.657  10.597  10395  Z= 0.353
  Chirality :  0.043   0.220   1075
  Planarity :  0.004   0.036   1344
  Dihedral  :  4.495  20.862    995
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.76 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.68 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.28), residues: 904
  helix:  1.58 (0.22), residues: 515
  sheet: -0.17 (0.97), residues: 24
  loop : -0.89 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 
 PHE   0.018   0.002   PHE A 220 
 TYR   0.019   0.002   TYR A 913 
 ARG   0.005   0.001   ARG A 300 

*********************** 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
  172 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ASN cc_start: 0.8903 (p0) cc_final: 0.8689 (p0)
REVERT: A  167 GLU cc_start: 0.8975 (tp30) cc_final: 0.8694 (mt-10)
REVERT: A  180 GLU cc_start: 0.8582 (tt0) cc_final: 0.8337 (tt0)
REVERT: A  194 ASP cc_start: 0.8847 (m-30) cc_final: 0.8368 (m-30)
REVERT: A  227 ASN cc_start: 0.8906 (t0) cc_final: 0.8609 (t0)
REVERT: A  514 LYS cc_start: 0.9272 (tttt) cc_final: 0.8556 (tttp)
REVERT: A  515 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7723 (mm-30)
REVERT: A  525 PHE cc_start: 0.8730 (t80) cc_final: 0.8529 (t80)
REVERT: A  625 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5777 (mp0)
REVERT: A  630 MET cc_start: 0.9141 (mmp) cc_final: 0.8827 (mmp)
REVERT: A  673 LYS cc_start: 0.9112 (tttt) cc_final: 0.8867 (tmtt)
REVERT: A  758 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8898 (tt0)
REVERT: A  774 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8680 (mmtm)
REVERT: A  883 GLU cc_start: 0.8171 (tt0) cc_final: 0.7513 (pp20)
REVERT: A  894 ARG cc_start: 0.7604 (ptt90) cc_final: 0.7193 (tmm-80)
REVERT: A  920 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8190 (t70)
REVERT: A  963 ASP cc_start: 0.8757 (m-30) cc_final: 0.7571 (t0)
REVERT: A  982 ASN cc_start: 0.8988 (m-40) cc_final: 0.8714 (m110)
REVERT: A 1014 GLN cc_start: 0.8357 (tt0) cc_final: 0.8080 (tt0)
REVERT: A 1017 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8341 (mtm180)
REVERT: A 1067 TYR cc_start: 0.9439 (t80) cc_final: 0.9217 (t80)
REVERT: A 1072 LYS cc_start: 0.9298 (pttm) cc_final: 0.9070 (pttm)
REVERT: A 1084 LYS cc_start: 0.9459 (mmtt) cc_final: 0.9173 (mmtt)
REVERT: A 1130 LYS cc_start: 0.8909 (mttt) cc_final: 0.8160 (tmmt)
  outliers start: 24
  outliers final: 16
  residues processed: 164
  average time/residue: 0.2097
  time to fit residues: 45.9835
Evaluate side-chains
  165 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  758 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue 1017 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 55 optimal weight:    0.2980
   chunk 84 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 43 optimal weight:    0.2980
   chunk 52 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0060
   overall best weight:    0.6598

-------------------------------------------------------------------------------
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 = 0.3874 r_free = 0.3874 target = 0.106815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.082391 restraints weight = 20817.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.085788 restraints weight = 11531.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.087967 restraints weight = 7921.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.6892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7734  Z= 0.193
  Angle     :  0.670  12.998  10395  Z= 0.355
  Chirality :  0.043   0.214   1075
  Planarity :  0.004   0.037   1344
  Dihedral  :  4.459  19.823    995
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.87 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.64 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.28), residues: 904
  helix:  1.69 (0.22), residues: 508
  sheet: -0.21 (0.99), residues: 24
  loop : -0.90 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 
 PHE   0.018   0.002   PHE A 220 
 TYR   0.020   0.002   TYR A 643 
 ARG   0.005   0.001   ARG A 300 

********************** 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
  167 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.843 
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   97 MET cc_start: 0.8603 (tpp) cc_final: 0.8131 (mmm)
REVERT: A   98 ASN cc_start: 0.8912 (p0) cc_final: 0.8701 (p0)
REVERT: A  167 GLU cc_start: 0.8975 (tp30) cc_final: 0.8712 (mt-10)
REVERT: A  180 GLU cc_start: 0.8604 (tt0) cc_final: 0.8288 (mt-10)
REVERT: A  194 ASP cc_start: 0.8779 (m-30) cc_final: 0.8339 (m-30)
REVERT: A  227 ASN cc_start: 0.8927 (t0) cc_final: 0.8647 (t0)
REVERT: A  514 LYS cc_start: 0.9270 (tttt) cc_final: 0.8607 (tttp)
REVERT: A  515 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7740 (mm-30)
REVERT: A  625 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5885 (mp0)
REVERT: A  630 MET cc_start: 0.9130 (mmp) cc_final: 0.8819 (mmp)
REVERT: A  673 LYS cc_start: 0.9079 (tttt) cc_final: 0.8838 (tmtt)
REVERT: A  774 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8637 (mmtm)
REVERT: A  883 GLU cc_start: 0.8161 (tt0) cc_final: 0.7707 (tp30)
REVERT: A  894 ARG cc_start: 0.7706 (ptt90) cc_final: 0.7287 (tmm-80)
REVERT: A  963 ASP cc_start: 0.8725 (m-30) cc_final: 0.7559 (t0)
REVERT: A  982 ASN cc_start: 0.9001 (m-40) cc_final: 0.8734 (m110)
REVERT: A 1014 GLN cc_start: 0.8376 (tt0) cc_final: 0.8138 (tt0)
REVERT: A 1017 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8093 (mtm180)
REVERT: A 1072 LYS cc_start: 0.9277 (pttm) cc_final: 0.9063 (pttm)
REVERT: A 1084 LYS cc_start: 0.9453 (mmtt) cc_final: 0.9168 (mmtt)
REVERT: A 1130 LYS cc_start: 0.8885 (mttt) cc_final: 0.8447 (tmtt)
  outliers start: 19
  outliers final: 14
  residues processed: 160
  average time/residue: 0.2075
  time to fit residues: 44.0343
Evaluate side-chains
  161 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  758 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue 1017 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0050
   chunk 20 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.6794

-------------------------------------------------------------------------------
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
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.107714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.083936 restraints weight = 20977.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.087438 restraints weight = 11235.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.089735 restraints weight = 7577.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.6990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7734  Z= 0.191
  Angle     :  0.661  12.681  10395  Z= 0.349
  Chirality :  0.042   0.179   1075
  Planarity :  0.004   0.038   1344
  Dihedral  :  4.402  20.074    995
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.20 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.77 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.27), residues: 904
  helix:  1.75 (0.22), residues: 506
  sheet: -0.24 (0.98), residues: 24
  loop : -1.06 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  18 
 PHE   0.016   0.002   PHE A 220 
 TYR   0.020   0.002   TYR A1034 
 ARG   0.005   0.000   ARG A 300 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3078.12 seconds
wall clock time: 54 minutes 15.18 seconds (3255.18 seconds total)