Starting phenix.real_space_refine
on Sat May 10 20:39:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t5s_41060/05_2025/8t5s_41060.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t5s_41060/05_2025/8t5s_41060.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t5s_41060/05_2025/8t5s_41060.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t5s_41060/05_2025/8t5s_41060.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t5s_41060/05_2025/8t5s_41060.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t5s_41060/05_2025/8t5s_41060.cif"
  }
  resolution = 2.9
  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=   0.019
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      62      5.49       5
     Mg      1      5.21       5
     S      40      5.16       5
     C    4017      2.51       5
     N    1187      2.21       5
     O    1491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6799
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 693, 5510
          Classifications: {'peptide': 693}
          Link IDs: {'PTRANS': 21, 'TRANS': 671}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 600
          Classifications: {'RNA': 30}
          Modifications used: {'rna3p_pyr': 30}
          Link IDs: {'rna3p': 29}
    Chain: "B"
      Number of atoms: 660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 660
          Classifications: {'RNA': 30}
          Modifications used: {'rna3p_pur': 30}
          Link IDs: {'rna3p': 29}
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4622  SG  CYS A 891      33.616  20.824  52.033  1.00141.13           S
  ATOM   4646  SG  CYS A 894      33.665  17.107  51.305  1.00141.12           S
  ATOM   4947  SG  CYS A 945      34.617  18.363  54.764  1.00143.31           S
  ATOM   4992  SG  CYS A 950      36.953  18.952  51.820  1.00149.53           S

  Time building chain proxies: 4.52, per 1000 atoms: 0.66
  Number of scatterers: 6799
  At special positions: 0
  Unit cell: (89.93, 96.278, 105.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      40     16.00
     P      62     15.00
     Mg      1     11.99
     O    1491      8.00
     N    1187      7.00
     C    4017      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.75
  Conformation dependent library (CDL) restraints added in 766.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 894 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 945 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 891 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 950 "
      Number of angles added : 6


  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1322

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 5 sheets defined
      54.3% alpha, 9.4% beta
      30 base pairs and 53 stacking pairs defined.
    Time for finding SS restraints: 2.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 305
      removed outlier: 3.549A  pdb=" N   VAL A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 339
    Processing helix  chain 'A' and resid 353 through 365
    Processing helix  chain 'A' and resid 381 through 389
      removed outlier: 3.711A  pdb=" N   VAL A 385 " --> pdb=" O   PRO A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 402
    Processing helix  chain 'A' and resid 420 through 424
      removed outlier: 3.743A  pdb=" N   PHE A 424 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 435
    Processing helix  chain 'A' and resid 439 through 454
    Processing helix  chain 'A' and resid 480 through 495
    Processing helix  chain 'A' and resid 506 through 514
    Processing helix  chain 'A' and resid 529 through 557
    Processing helix  chain 'A' and resid 589 through 605
      removed outlier: 4.248A  pdb=" N   GLN A 593 " --> pdb=" O   HIS A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 637
      removed outlier: 3.902A  pdb=" N   ARG A 614 " --> pdb=" O   GLU A 610 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   THR A 615 " --> pdb=" O   THR A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 654
      removed outlier: 3.991A  pdb=" N   ALA A 642 " --> pdb=" O   HIS A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 657
      No H-bonds generated for 'chain 'A' and resid 655 through 657'
    Processing helix  chain 'A' and resid 658 through 676
      removed outlier: 3.846A  pdb=" N   GLY A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 697
    Processing helix  chain 'A' and resid 708 through 721
    Processing helix  chain 'A' and resid 722 through 728
      removed outlier: 4.175A  pdb=" N   LEU A 728 " --> pdb=" O   GLU A 724 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 764
    Processing helix  chain 'A' and resid 773 through 778
      removed outlier: 3.526A  pdb=" N   GLU A 778 " --> pdb=" O   VAL A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 806
    Processing helix  chain 'A' and resid 820 through 847
      removed outlier: 3.614A  pdb=" N   ARG A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 859
    Processing helix  chain 'A' and resid 861 through 881
      removed outlier: 3.558A  pdb=" N   ILE A 866 " --> pdb=" O   ILE A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 915 through 919
      removed outlier: 4.218A  pdb=" N   TRP A 919 " --> pdb=" O   PRO A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 988 through 996
      removed outlier: 3.873A  pdb=" N   ILE A 992 " --> pdb=" O   LYS A 988 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1014
      removed outlier: 3.653A  pdb=" N   THR A1009 " --> pdb=" O   LEU A1005 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP A1012 " --> pdb=" O   GLN A1008 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ASP A1014 " --> pdb=" O   MET A1010 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 374
      removed outlier: 3.657A  pdb=" N   GLN A 372 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ALA A 344 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   ALA A 394 " --> pdb=" O   ALA A 344 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   PHE A 346 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   MET A 347 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   THR A 310 " --> pdb=" O   ILE A 466 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE A 311 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 519 through 523
      removed outlier: 3.747A  pdb=" N   VAL A 771 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 890 through 891
    Processing sheet with id=AA4, first strand: chain 'A' and resid 911 through 913
      removed outlier: 4.204A  pdb=" N   THR A1000 " --> pdb=" O   ILE A 904 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 943 through 944
      removed outlier: 3.736A  pdb=" N   GLY A 955 " --> pdb=" O   ILE A 943 " (cutoff:3.500A)

    291 hydrogen bonds defined for protein.
    852 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      60 hydrogen bonds
      120 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      53 stacking parallelities
  Total time for adding SS restraints: 3.00

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2040
        1.34 -     1.46: 1372
        1.46 -     1.58: 3434
        1.58 -     1.70: 121
        1.70 -     1.81: 60
  Bond restraints: 7027
  Sorted by residual:
  bond pdb=" C   TRP A 863 "
       pdb=" N   PRO A 864 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.020 1.28e-02 6.10e+03 2.55e+00
  bond pdb=" C4  ADP A1103 "
       pdb=" C5  ADP A1103 "
    ideal  model  delta    sigma   weight residual
    1.490  1.464  0.026 2.00e-02 2.50e+03 1.68e+00
  bond pdb=" CA  ASN A 884 "
       pdb=" CB  ASN A 884 "
    ideal  model  delta    sigma   weight residual
    1.532  1.549 -0.017 1.56e-02 4.11e+03 1.18e+00
  bond pdb=" CB  ASN A 884 "
       pdb=" CG  ASN A 884 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  bond pdb=" CB  GLU A 948 "
       pdb=" CG  GLU A 948 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.28e-01
  ... (remaining 7022 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 9641
        1.82 -     3.64: 103
        3.64 -     5.46: 19
        5.46 -     7.28: 8
        7.28 -     9.11: 3
  Bond angle restraints: 9774
  Sorted by residual:
  angle pdb=" CB  MET A 650 "
        pdb=" CG  MET A 650 "
        pdb=" SD  MET A 650 "
      ideal   model   delta    sigma   weight residual
     112.70  121.81   -9.11 3.00e+00 1.11e-01 9.21e+00
  angle pdb=" C   ARG A 883 "
        pdb=" N   ASN A 884 "
        pdb=" CA  ASN A 884 "
      ideal   model   delta    sigma   weight residual
     123.05  127.75   -4.70 1.57e+00 4.06e-01 8.96e+00
  angle pdb=" CA  ARG A 865 "
        pdb=" CB  ARG A 865 "
        pdb=" CG  ARG A 865 "
      ideal   model   delta    sigma   weight residual
     114.10  119.68   -5.58 2.00e+00 2.50e-01 7.78e+00
  angle pdb=" CB  ARG A 865 "
        pdb=" CG  ARG A 865 "
        pdb=" CD  ARG A 865 "
      ideal   model   delta    sigma   weight residual
     111.30  117.55   -6.25 2.30e+00 1.89e-01 7.37e+00
  angle pdb=" CB  MET A 445 "
        pdb=" CG  MET A 445 "
        pdb=" SD  MET A 445 "
      ideal   model   delta    sigma   weight residual
     112.70  120.79   -8.09 3.00e+00 1.11e-01 7.27e+00
  ... (remaining 9769 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.41: 3849
       21.41 -    42.82: 360
       42.82 -    64.23: 83
       64.23 -    85.64: 7
       85.64 -   107.05: 4
  Dihedral angle restraints: 4303
    sinusoidal: 2272
      harmonic: 2031
  Sorted by residual:
  dihedral pdb=" O2A ADP A1103 "
           pdb=" O3A ADP A1103 "
           pdb=" PA  ADP A1103 "
           pdb=" PB  ADP A1103 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -167.05  107.05     1      2.00e+01 2.50e-03 3.10e+01
  dihedral pdb=" O1B ADP A1103 "
           pdb=" O3A ADP A1103 "
           pdb=" PB  ADP A1103 "
           pdb=" PA  ADP A1103 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00    8.24  -68.24     1      2.00e+01 2.50e-03 1.51e+01
  dihedral pdb=" C4' ADP A1103 "
           pdb=" C5' ADP A1103 "
           pdb=" O5' ADP A1103 "
           pdb=" PA  ADP A1103 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  114.28   65.72     1      2.00e+01 2.50e-03 1.41e+01
  ... (remaining 4300 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 877
       0.029 -    0.059: 175
       0.059 -    0.088: 76
       0.088 -    0.118: 41
       0.118 -    0.147: 4
  Chirality restraints: 1173
  Sorted by residual:
  chirality pdb=" CA  ASN A 884 "
            pdb=" N   ASN A 884 "
            pdb=" C   ASN A 884 "
            pdb=" CB  ASN A 884 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.43e-01
  chirality pdb=" CB  THR A 552 "
            pdb=" CA  THR A 552 "
            pdb=" OG1 THR A 552 "
            pdb=" CG2 THR A 552 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  TRP A 863 "
            pdb=" N   TRP A 863 "
            pdb=" C   TRP A 863 "
            pdb=" CB  TRP A 863 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.74e-01
  ... (remaining 1170 not shown)

  Planarity restraints: 1037
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 863 "   -0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO A 864 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 864 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 864 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 883 "    0.005 2.00e-02 2.50e+03   1.09e-02 1.20e+00
        pdb=" C   ARG A 883 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ARG A 883 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ASN A 884 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 638 "   -0.017 5.00e-02 4.00e+02   2.58e-02 1.06e+00
        pdb=" N   PRO A 639 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 639 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 639 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1034 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 768
        2.75 -     3.29: 6519
        3.29 -     3.82: 12585
        3.82 -     4.36: 13656
        4.36 -     4.90: 21943
  Nonbonded interactions: 55471
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 908 "
            pdb=" O2'   A B  36 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" N   GLU A 948 "
            pdb=" OE1 GLU A 948 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OG1 THR A 742 "
            pdb=" OP2   A B  30 "
     model   vdw
     2.247 3.040
  nonbonded pdb="MG    MG A1102 "
            pdb=" O3B ADP A1103 "
     model   vdw
     2.299 2.170
  nonbonded pdb=" N   GLU A 778 "
            pdb=" OE1 GLU A 778 "
     model   vdw
     2.314 3.120
  ... (remaining 55466 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.370
  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:10.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
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      :  0.002   0.029   7031  Z= 0.097
  Angle     :  0.500   9.106   9780  Z= 0.242
  Chirality :  0.034   0.147   1173
  Planarity :  0.003   0.044   1037
  Dihedral  : 16.224 107.051   2981
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 30.73 %
    Favored  : 68.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.43 (0.33), residues: 685
  helix:  2.94 (0.27), residues: 340
  sheet:  0.96 (0.65), residues: 75
  loop :  0.08 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 734 
 HIS   0.003   0.000   HIS A 638 
 PHE   0.007   0.001   PHE A 762 
 TYR   0.008   0.001   TYR A 911 
 ARG   0.004   0.000   ARG A 868 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13946 (  351)
  hydrogen bonds       : angle       5.16165 (  972)
  metal coordination   : bond        0.00148 (    4)
  metal coordination   : angle       0.54081 (    6)
  covalent geometry    : bond        0.00195 ( 7027)
  covalent geometry    : angle       0.49993 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  702 THR cc_start: 0.8298 (m) cc_final: 0.8024 (p)
REVERT: A  893 LYS cc_start: 0.8175 (tttt) cc_final: 0.7956 (mtpt)
REVERT: A 1010 MET cc_start: 0.7787 (ttm) cc_final: 0.7102 (ttp)
  outliers start: 5
  outliers final: 2
  residues processed: 70
  average time/residue: 0.8476
  time to fit residues: 63.9863
Evaluate side-chains
  61 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  550 ILE
Chi-restraints excluded: chain A residue  992 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   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 326 ASN
A 506 ASN
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 694 ASN
A 908 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.104765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.079813 restraints weight = 14050.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 3.06
r_work: 0.3212 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7031  Z= 0.147
  Angle     :  0.521   6.149   9780  Z= 0.258
  Chirality :  0.037   0.153   1173
  Planarity :  0.004   0.043   1037
  Dihedral  : 11.146  59.220   1600
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 24.04 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.38 (0.33), residues: 685
  helix:  2.85 (0.28), residues: 346
  sheet:  1.08 (0.64), residues: 75
  loop : -0.01 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 863 
 HIS   0.004   0.001   HIS A 449 
 PHE   0.011   0.001   PHE A 762 
 TYR   0.012   0.001   TYR A 911 
 ARG   0.007   0.000   ARG A 868 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03397 (  351)
  hydrogen bonds       : angle       4.07825 (  972)
  metal coordination   : bond        0.00511 (    4)
  metal coordination   : angle       2.33844 (    6)
  covalent geometry    : bond        0.00315 ( 7027)
  covalent geometry    : angle       0.51817 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 66
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: A  504 LYS cc_start: 0.8219 (tppt) cc_final: 0.8018 (mptt)
REVERT: A  534 MET cc_start: 0.7684 (tpt) cc_final: 0.7413 (tpt)
REVERT: A  735 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8372 (tpt)
REVERT: A 1011 ARG cc_start: 0.8555 (mmp-170) cc_final: 0.8289 (mmp80)
  outliers start: 32
  outliers final: 15
  residues processed: 90
  average time/residue: 0.7941
  time to fit residues: 77.4110
Evaluate side-chains
  78 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  735 MET
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain A residue  868 ARG
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  985 ILE
Chi-restraints excluded: chain A residue  992 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 25 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 GLN
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.096361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.070678 restraints weight = 14210.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.90
r_work: 0.3034 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7031  Z= 0.168
  Angle     :  0.550   8.442   9780  Z= 0.271
  Chirality :  0.038   0.140   1173
  Planarity :  0.003   0.039   1037
  Dihedral  : 11.238  58.705   1598
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 24.20 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.89 (0.33), residues: 685
  helix:  2.38 (0.27), residues: 350
  sheet:  0.72 (0.60), residues: 80
  loop : -0.14 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 989 
 HIS   0.005   0.001   HIS A 406 
 PHE   0.012   0.001   PHE A 346 
 TYR   0.013   0.001   TYR A 911 
 ARG   0.006   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03553 (  351)
  hydrogen bonds       : angle       4.08000 (  972)
  metal coordination   : bond        0.00657 (    4)
  metal coordination   : angle       3.13290 (    6)
  covalent geometry    : bond        0.00364 ( 7027)
  covalent geometry    : angle       0.54449 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 63
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
REVERT: A  454 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7458 (mtm)
REVERT: A  472 SER cc_start: 0.8873 (t) cc_final: 0.8515 (t)
REVERT: A  534 MET cc_start: 0.7750 (tpt) cc_final: 0.7443 (tpt)
REVERT: A  543 MET cc_start: 0.7944 (mmt) cc_final: 0.7599 (mmt)
REVERT: A  544 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7810 (mp10)
REVERT: A  609 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8359 (ttm170)
REVERT: A  735 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8434 (tpt)
REVERT: A  837 MET cc_start: 0.8656 (tpp) cc_final: 0.8450 (tpp)
REVERT: A  863 TRP cc_start: 0.4556 (OUTLIER) cc_final: 0.2994 (p90)
REVERT: A  921 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7434 (pp)
  outliers start: 34
  outliers final: 14
  residues processed: 86
  average time/residue: 0.9549
  time to fit residues: 87.5648
Evaluate side-chains
  65 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  544 GLN
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  667 ARG
Chi-restraints excluded: chain A residue  711 GLU
Chi-restraints excluded: chain A residue  735 MET
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  863 TRP
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  985 ILE
Chi-restraints excluded: chain A residue  992 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 GLN
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 908 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.093927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.068627 restraints weight = 14305.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.87
r_work: 0.2996 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7031  Z= 0.167
  Angle     :  0.550  10.192   9780  Z= 0.268
  Chirality :  0.038   0.151   1173
  Planarity :  0.004   0.039   1037
  Dihedral  : 11.287  59.768   1598
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 23.09 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.80 (0.33), residues: 685
  helix:  2.32 (0.28), residues: 351
  sheet:  0.39 (0.59), residues: 80
  loop : -0.11 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 863 
 HIS   0.003   0.001   HIS A 449 
 PHE   0.008   0.001   PHE A 429 
 TYR   0.011   0.001   TYR A 668 
 ARG   0.003   0.000   ARG A1011 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03488 (  351)
  hydrogen bonds       : angle       4.04444 (  972)
  metal coordination   : bond        0.00674 (    4)
  metal coordination   : angle       3.10773 (    6)
  covalent geometry    : bond        0.00365 ( 7027)
  covalent geometry    : angle       0.54489 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 50
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: A  454 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7517 (mtt)
REVERT: A  472 SER cc_start: 0.8969 (t) cc_final: 0.8618 (t)
REVERT: A  534 MET cc_start: 0.7620 (tpt) cc_final: 0.7307 (tpt)
REVERT: A  543 MET cc_start: 0.8066 (mmt) cc_final: 0.7817 (mmt)
REVERT: A  544 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7861 (mp10)
REVERT: A  547 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7895 (mm-30)
REVERT: A  609 ARG cc_start: 0.8638 (ttm170) cc_final: 0.8356 (ttm170)
REVERT: A  661 MET cc_start: 0.8372 (tpt) cc_final: 0.7991 (tpt)
REVERT: A  863 TRP cc_start: 0.4885 (OUTLIER) cc_final: 0.3661 (p90)
REVERT: A  865 ARG cc_start: 0.7532 (mmp-170) cc_final: 0.7201 (mmp-170)
REVERT: A 1011 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8388 (mmp80)
  outliers start: 36
  outliers final: 12
  residues processed: 73
  average time/residue: 1.0105
  time to fit residues: 78.8457
Evaluate side-chains
  61 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  544 GLN
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  711 GLU
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain A residue  863 TRP
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  985 ILE
Chi-restraints excluded: chain A residue  992 ILE
Chi-restraints excluded: chain A residue 1011 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0170
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 845 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.094623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.069599 restraints weight = 14214.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.83
r_work: 0.3012 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7031  Z= 0.122
  Angle     :  0.529  11.188   9780  Z= 0.256
  Chirality :  0.037   0.176   1173
  Planarity :  0.003   0.033   1037
  Dihedral  : 11.294  58.449   1598
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 23.57 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.74 (0.33), residues: 685
  helix:  2.26 (0.27), residues: 355
  sheet:  0.33 (0.58), residues: 80
  loop : -0.16 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 734 
 HIS   0.003   0.001   HIS A 638 
 PHE   0.007   0.001   PHE A 429 
 TYR   0.010   0.001   TYR A 911 
 ARG   0.007   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03122 (  351)
  hydrogen bonds       : angle       3.94030 (  972)
  metal coordination   : bond        0.00433 (    4)
  metal coordination   : angle       2.56845 (    6)
  covalent geometry    : bond        0.00268 ( 7027)
  covalent geometry    : angle       0.52496 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 55
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
REVERT: A  454 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7481 (mtt)
REVERT: A  472 SER cc_start: 0.8884 (t) cc_final: 0.8535 (t)
REVERT: A  504 LYS cc_start: 0.8491 (tppt) cc_final: 0.8273 (tppt)
REVERT: A  534 MET cc_start: 0.7600 (tpt) cc_final: 0.7293 (tpt)
REVERT: A  543 MET cc_start: 0.8117 (mmt) cc_final: 0.7809 (mmt)
REVERT: A  544 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7827 (mp10)
REVERT: A  547 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7898 (mm-30)
REVERT: A  609 ARG cc_start: 0.8646 (ttm170) cc_final: 0.8367 (ttm170)
REVERT: A  661 MET cc_start: 0.8419 (tpt) cc_final: 0.8042 (tpt)
REVERT: A  863 TRP cc_start: 0.4606 (OUTLIER) cc_final: 0.2588 (p90)
REVERT: A  921 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7631 (pp)
REVERT: A 1011 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8500 (mmp80)
  outliers start: 32
  outliers final: 13
  residues processed: 80
  average time/residue: 1.1297
  time to fit residues: 95.7513
Evaluate side-chains
  67 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  544 GLN
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  667 ARG
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain A residue  863 TRP
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  985 ILE
Chi-restraints excluded: chain A residue  992 ILE
Chi-restraints excluded: chain A residue 1011 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 69 optimal weight:    8.9990
   chunk 40 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 908 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 = 0.3577 r_free = 0.3577 target = 0.092727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.067605 restraints weight = 14181.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.82
r_work: 0.2974 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7031  Z= 0.158
  Angle     :  0.556  11.204   9780  Z= 0.273
  Chirality :  0.038   0.161   1173
  Planarity :  0.004   0.049   1037
  Dihedral  : 11.283  58.654   1598
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 24.20 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.68 (0.33), residues: 685
  helix:  2.21 (0.27), residues: 355
  sheet:  0.27 (0.59), residues: 80
  loop : -0.15 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 989 
 HIS   0.003   0.001   HIS A 638 
 PHE   0.007   0.001   PHE A 429 
 TYR   0.011   0.001   TYR A 668 
 ARG   0.005   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  351)
  hydrogen bonds       : angle       4.04279 (  972)
  metal coordination   : bond        0.00665 (    4)
  metal coordination   : angle       3.14607 (    6)
  covalent geometry    : bond        0.00347 ( 7027)
  covalent geometry    : angle       0.55107 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 46
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
REVERT: A  454 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7592 (mtt)
REVERT: A  472 SER cc_start: 0.8912 (t) cc_final: 0.8566 (t)
REVERT: A  534 MET cc_start: 0.7575 (tpt) cc_final: 0.7267 (tpt)
REVERT: A  544 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7873 (mp10)
REVERT: A  609 ARG cc_start: 0.8713 (ttm170) cc_final: 0.8425 (ttm170)
REVERT: A  863 TRP cc_start: 0.4907 (OUTLIER) cc_final: 0.2704 (p90)
REVERT: A  921 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7753 (pp)
REVERT: A 1011 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8531 (mmp80)
  outliers start: 30
  outliers final: 15
  residues processed: 71
  average time/residue: 1.1197
  time to fit residues: 84.3162
Evaluate side-chains
  61 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 41
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain A residue  461 HIS
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  544 GLN
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  667 ARG
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain A residue  863 TRP
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  985 ILE
Chi-restraints excluded: chain A residue  992 ILE
Chi-restraints excluded: chain A residue 1011 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 69 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 61 optimal weight:    0.2980
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 908 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 = 0.3596 r_free = 0.3596 target = 0.093700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.068576 restraints weight = 14166.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.86
r_work: 0.2996 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7031  Z= 0.121
  Angle     :  0.556  11.006   9780  Z= 0.271
  Chirality :  0.037   0.232   1173
  Planarity :  0.003   0.031   1037
  Dihedral  : 11.301  58.431   1598
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 25.16 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.72 (0.33), residues: 685
  helix:  2.26 (0.27), residues: 355
  sheet:  0.26 (0.58), residues: 80
  loop : -0.16 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 734 
 HIS   0.003   0.001   HIS A 638 
 PHE   0.007   0.001   PHE A 762 
 TYR   0.010   0.001   TYR A 911 
 ARG   0.007   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03189 (  351)
  hydrogen bonds       : angle       3.95828 (  972)
  metal coordination   : bond        0.00431 (    4)
  metal coordination   : angle       2.43159 (    6)
  covalent geometry    : bond        0.00262 ( 7027)
  covalent geometry    : angle       0.55301 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 46
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
REVERT: A  454 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7497 (mtt)
REVERT: A  472 SER cc_start: 0.8719 (t) cc_final: 0.8389 (t)
REVERT: A  534 MET cc_start: 0.7544 (tpt) cc_final: 0.7231 (tpt)
REVERT: A  609 ARG cc_start: 0.8774 (ttm170) cc_final: 0.8503 (ttm170)
REVERT: A  764 ASP cc_start: 0.8572 (m-30) cc_final: 0.8315 (m-30)
REVERT: A  863 TRP cc_start: 0.4845 (OUTLIER) cc_final: 0.2806 (p90)
REVERT: A  921 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7714 (pp)
REVERT: A 1011 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8560 (mmp80)
  outliers start: 25
  outliers final: 13
  residues processed: 66
  average time/residue: 1.0514
  time to fit residues: 73.9190
Evaluate side-chains
  59 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain A residue  461 HIS
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  667 ARG
Chi-restraints excluded: chain A residue  711 GLU
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain A residue  863 TRP
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  985 ILE
Chi-restraints excluded: chain A residue  992 ILE
Chi-restraints excluded: chain A residue 1011 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0470
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 908 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.092924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.068002 restraints weight = 14234.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 2.81
r_work: 0.2984 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.4172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7031  Z= 0.131
  Angle     :  0.552   8.973   9780  Z= 0.271
  Chirality :  0.038   0.293   1173
  Planarity :  0.003   0.031   1037
  Dihedral  : 11.278  58.484   1598
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 26.43 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.79 (0.33), residues: 685
  helix:  2.34 (0.27), residues: 351
  sheet:  0.24 (0.58), residues: 80
  loop : -0.09 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 734 
 HIS   0.003   0.001   HIS A 638 
 PHE   0.007   0.001   PHE A 429 
 TYR   0.012   0.001   TYR A 793 
 ARG   0.008   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  351)
  hydrogen bonds       : angle       3.93702 (  972)
  metal coordination   : bond        0.00489 (    4)
  metal coordination   : angle       2.49091 (    6)
  covalent geometry    : bond        0.00286 ( 7027)
  covalent geometry    : angle       0.54910 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 45
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7649 (mtt)
REVERT: A  472 SER cc_start: 0.8845 (t) cc_final: 0.8498 (t)
REVERT: A  534 MET cc_start: 0.7487 (tpt) cc_final: 0.7274 (tpt)
REVERT: A  609 ARG cc_start: 0.8759 (ttm170) cc_final: 0.8492 (ttm170)
REVERT: A  661 MET cc_start: 0.8585 (tpt) cc_final: 0.8306 (tpt)
REVERT: A  759 LEU cc_start: 0.9086 (mt) cc_final: 0.8812 (mp)
REVERT: A  764 ASP cc_start: 0.8583 (m-30) cc_final: 0.8334 (m-30)
REVERT: A  863 TRP cc_start: 0.5015 (OUTLIER) cc_final: 0.2567 (p90)
REVERT: A  921 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7764 (pp)
REVERT: A 1011 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8584 (mmp80)
  outliers start: 23
  outliers final: 12
  residues processed: 63
  average time/residue: 1.0511
  time to fit residues: 70.5021
Evaluate side-chains
  60 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain A residue  461 HIS
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain A residue  667 ARG
Chi-restraints excluded: chain A residue  711 GLU
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain A residue  863 TRP
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  985 ILE
Chi-restraints excluded: chain A residue  992 ILE
Chi-restraints excluded: chain A residue 1011 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   chunk 39 optimal weight:    0.0980
   chunk 11 optimal weight:    0.8980
   chunk 58 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 1 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 908 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.094422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.069428 restraints weight = 14253.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.92
r_work: 0.3010 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7031  Z= 0.110
  Angle     :  0.568  13.768   9780  Z= 0.273
  Chirality :  0.038   0.331   1173
  Planarity :  0.003   0.029   1037
  Dihedral  : 11.273  58.307   1598
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 27.23 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.89 (0.33), residues: 685
  helix:  2.40 (0.27), residues: 351
  sheet:  0.39 (0.63), residues: 70
  loop : -0.05 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 734 
 HIS   0.003   0.001   HIS A 638 
 PHE   0.007   0.001   PHE A 997 
 TYR   0.010   0.001   TYR A 911 
 ARG   0.009   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03048 (  351)
  hydrogen bonds       : angle       3.86889 (  972)
  metal coordination   : bond        0.00367 (    4)
  metal coordination   : angle       2.07761 (    6)
  covalent geometry    : bond        0.00238 ( 7027)
  covalent geometry    : angle       0.56584 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
REVERT: A  454 MET cc_start: 0.7800 (mmm) cc_final: 0.7540 (mtt)
REVERT: A  472 SER cc_start: 0.8587 (t) cc_final: 0.8258 (t)
REVERT: A  534 MET cc_start: 0.7532 (tpt) cc_final: 0.7327 (tpt)
REVERT: A  609 ARG cc_start: 0.8751 (ttm170) cc_final: 0.8481 (ttm170)
REVERT: A  764 ASP cc_start: 0.8574 (m-30) cc_final: 0.8323 (m-30)
REVERT: A  863 TRP cc_start: 0.5023 (OUTLIER) cc_final: 0.2561 (p90)
REVERT: A  870 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8915 (p0)
REVERT: A  921 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7625 (pp)
REVERT: A 1011 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8553 (mmp80)
  outliers start: 16
  outliers final: 11
  residues processed: 60
  average time/residue: 1.0961
  time to fit residues: 69.8428
Evaluate side-chains
  60 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  461 HIS
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain A residue  667 ARG
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain A residue  863 TRP
Chi-restraints excluded: chain A residue  870 ASP
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  985 ILE
Chi-restraints excluded: chain A residue  992 ILE
Chi-restraints excluded: chain A residue 1011 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0670
   chunk 51 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0030
   chunk 33 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    0.4128

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

Flipped N/Q/H residues before XYZ refinement:
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.094300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.069379 restraints weight = 14406.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.89
r_work: 0.3012 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.4182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7031  Z= 0.111
  Angle     :  0.570  13.509   9780  Z= 0.275
  Chirality :  0.037   0.190   1173
  Planarity :  0.003   0.030   1037
  Dihedral  : 11.256  58.327   1598
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.75 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.84 (0.33), residues: 685
  helix:  2.40 (0.27), residues: 351
  sheet:  0.49 (0.58), residues: 78
  loop : -0.20 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 734 
 HIS   0.003   0.001   HIS A 638 
 PHE   0.006   0.001   PHE A 997 
 TYR   0.010   0.001   TYR A 911 
 ARG   0.007   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03020 (  351)
  hydrogen bonds       : angle       3.86718 (  972)
  metal coordination   : bond        0.00357 (    4)
  metal coordination   : angle       2.08189 (    6)
  covalent geometry    : bond        0.00242 ( 7027)
  covalent geometry    : angle       0.56777 ( 9774)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 52
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 MET cc_start: 0.7794 (mmm) cc_final: 0.7535 (mtt)
REVERT: A  472 SER cc_start: 0.8569 (t) cc_final: 0.8260 (t)
REVERT: A  534 MET cc_start: 0.7532 (tpt) cc_final: 0.7325 (tpt)
REVERT: A  609 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8493 (ttm170)
REVERT: A  764 ASP cc_start: 0.8547 (m-30) cc_final: 0.8294 (m-30)
REVERT: A  863 TRP cc_start: 0.4947 (OUTLIER) cc_final: 0.2428 (p90)
REVERT: A  921 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7601 (pp)
REVERT: A 1011 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8575 (mmp80)
  outliers start: 18
  outliers final: 13
  residues processed: 66
  average time/residue: 1.0711
  time to fit residues: 75.1472
Evaluate side-chains
  60 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  461 HIS
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain A residue  667 ARG
Chi-restraints excluded: chain A residue  735 MET
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain A residue  863 TRP
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  922 VAL
Chi-restraints excluded: chain A residue  985 ILE
Chi-restraints excluded: chain A residue  992 ILE
Chi-restraints excluded: chain A residue 1011 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 875 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.092459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.067390 restraints weight = 14347.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.81
r_work: 0.2971 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.4308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7031  Z= 0.153
  Angle     :  0.589  10.753   9780  Z= 0.288
  Chirality :  0.037   0.178   1173
  Planarity :  0.004   0.035   1037
  Dihedral  : 11.258  58.526   1598
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 26.43 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.77 (0.33), residues: 685
  helix:  2.24 (0.27), residues: 357
  sheet:  0.41 (0.59), residues: 78
  loop : -0.10 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 734 
 HIS   0.003   0.001   HIS A 638 
 PHE   0.008   0.001   PHE A 429 
 TYR   0.017   0.001   TYR A 793 
 ARG   0.008   0.000   ARG A 868 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  351)
  hydrogen bonds       : angle       3.97193 (  972)
  metal coordination   : bond        0.00581 (    4)
  metal coordination   : angle       2.57209 (    6)
  covalent geometry    : bond        0.00339 ( 7027)
  covalent geometry    : angle       0.58585 ( 9774)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3910.73 seconds
wall clock time: 68 minutes 41.31 seconds (4121.31 seconds total)