Starting phenix.real_space_refine
on Sat May 10 01:16:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sym_40884/05_2025/8sym_40884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sym_40884/05_2025/8sym_40884.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sym_40884/05_2025/8sym_40884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sym_40884/05_2025/8sym_40884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sym_40884/05_2025/8sym_40884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sym_40884/05_2025/8sym_40884.cif"
  }
  resolution = 3.2
  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=   0.014
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      27      5.16       5
     C    2878      2.51       5
     N     772      2.21       5
     O     809      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4486
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 376, 3023
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 12, 'TRANS': 363}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1463
          Classifications: {'peptide': 184}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 175}
  Time building chain proxies: 3.70, per 1000 atoms: 0.82
  Number of scatterers: 4486
  At special positions: 0
  Unit cell: (76.4928, 89.2416, 74.368, 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      27     16.00
     O     809      8.00
     N     772      7.00
     C    2878      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: 1.24
  Conformation dependent library (CDL) restraints added in 562.9 milliseconds
  

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1066

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 3 sheets defined
      54.8% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
    Processing helix  chain 'A' and resid 582 through 597
      removed outlier: 4.084A  pdb=" N   CYS A 586 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 619
    Processing helix  chain 'A' and resid 626 through 643
      removed outlier: 3.819A  pdb=" N   MET A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 664
    Processing helix  chain 'A' and resid 667 through 689
      removed outlier: 3.552A  pdb=" N   LEU A 671 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 712
      removed outlier: 3.998A  pdb=" N   ALA A 699 " --> pdb=" O   ARG A 695 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A 700 " --> pdb=" O   LYS A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 715
      No H-bonds generated for 'chain 'A' and resid 713 through 715'
    Processing helix  chain 'A' and resid 717 through 734
    Processing helix  chain 'A' and resid 737 through 752
    Processing helix  chain 'A' and resid 753 through 755
      No H-bonds generated for 'chain 'A' and resid 753 through 755'
    Processing helix  chain 'A' and resid 768 through 783
    Processing helix  chain 'A' and resid 795 through 808
    Processing helix  chain 'A' and resid 815 through 832
      removed outlier: 3.642A  pdb=" N   HIS A 826 " --> pdb=" O   THR A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 850
    Processing helix  chain 'A' and resid 853 through 882
    Processing helix  chain 'A' and resid 883 through 902
      removed outlier: 3.653A  pdb=" N   GLN A 887 " --> pdb=" O   ALA A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 906 through 923
      removed outlier: 3.820A  pdb=" N   HIS A 923 " --> pdb=" O   LEU A 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 30
      removed outlier: 3.576A  pdb=" N   LYS B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 55
      removed outlier: 3.729A  pdb=" N   TYR B  50 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 111
      removed outlier: 3.940A  pdb=" N   LEU B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26
      removed outlier: 6.463A  pdb=" N   LEU B   6 " --> pdb=" O   HIS B  37 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   LEU B  39 " --> pdb=" O   LEU B   6 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   LEU B   8 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 758 through 761
    Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81

    264 hydrogen bonds defined for protein.
    768 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.45 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: 1460
        1.34 -     1.46: 861
        1.46 -     1.57: 2224
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 4585
  Sorted by residual:
  bond pdb=" C   GLN B  93 "
       pdb=" N   VAL B  94 "
    ideal  model  delta    sigma   weight residual
    1.333  1.321  0.012 1.20e-02 6.94e+03 1.03e+00
  bond pdb=" CB  VAL B 112 "
       pdb=" CG2 VAL B 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.46e-01
  bond pdb=" CG1 ILE A 805 "
       pdb=" CD1 ILE A 805 "
    ideal  model  delta    sigma   weight residual
    1.513  1.478  0.035 3.90e-02 6.57e+02 7.90e-01
  bond pdb=" N   VAL B  63 "
       pdb=" CA  VAL B  63 "
    ideal  model  delta    sigma   weight residual
    1.454  1.444  0.010 1.28e-02 6.10e+03 5.91e-01
  bond pdb=" CA  HIS A 901 "
       pdb=" CB  HIS A 901 "
    ideal  model  delta    sigma   weight residual
    1.537  1.524  0.012 1.67e-02 3.59e+03 5.37e-01
  ... (remaining 4580 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 6045
        1.42 -     2.84: 129
        2.84 -     4.26: 19
        4.26 -     5.68: 5
        5.68 -     7.10: 3
  Bond angle restraints: 6201
  Sorted by residual:
  angle pdb=" C   LEU B  44 "
        pdb=" N   CYS B  45 "
        pdb=" CA  CYS B  45 "
      ideal   model   delta    sigma   weight residual
     121.54  128.64   -7.10 1.91e+00 2.74e-01 1.38e+01
  angle pdb=" C   VAL A 752 "
        pdb=" CA  VAL A 752 "
        pdb=" CB  VAL A 752 "
      ideal   model   delta    sigma   weight residual
     113.70  110.33    3.37 9.50e-01 1.11e+00 1.26e+01
  angle pdb=" N   GLY B 118 "
        pdb=" CA  GLY B 118 "
        pdb=" C   GLY B 118 "
      ideal   model   delta    sigma   weight residual
     113.18  120.08   -6.90 2.37e+00 1.78e-01 8.47e+00
  angle pdb=" C   ALA A 900 "
        pdb=" N   HIS A 901 "
        pdb=" CA  HIS A 901 "
      ideal   model   delta    sigma   weight residual
     122.42  118.86    3.56 1.77e+00 3.19e-01 4.03e+00
  angle pdb=" C   LEU A 751 "
        pdb=" N   VAL A 752 "
        pdb=" CA  VAL A 752 "
      ideal   model   delta    sigma   weight residual
     120.43  122.23   -1.80 9.60e-01 1.09e+00 3.51e+00
  ... (remaining 6196 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.30: 2466
       16.30 -    32.61: 218
       32.61 -    48.91: 57
       48.91 -    65.21: 4
       65.21 -    81.52: 6
  Dihedral angle restraints: 2751
    sinusoidal: 1110
      harmonic: 1641
  Sorted by residual:
  dihedral pdb=" CA  MET A 689 "
           pdb=" C   MET A 689 "
           pdb=" N   LYS A 690 "
           pdb=" CA  LYS A 690 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.23   18.77     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  HIS A  33 "
           pdb=" C   HIS A  33 "
           pdb=" N   PRO A  34 "
           pdb=" CA  PRO A  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.07  -16.93     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  TYR A  32 "
           pdb=" C   TYR A  32 "
           pdb=" N   HIS A  33 "
           pdb=" CA  HIS A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.71   16.29     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 2748 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 443
       0.034 -    0.068: 168
       0.068 -    0.101: 57
       0.101 -    0.135: 30
       0.135 -    0.169: 2
  Chirality restraints: 700
  Sorted by residual:
  chirality pdb=" CB  ILE A 718 "
            pdb=" CA  ILE A 718 "
            pdb=" CG1 ILE A 718 "
            pdb=" CG2 ILE A 718 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.13e-01
  chirality pdb=" CA  PRO A  34 "
            pdb=" N   PRO A  34 "
            pdb=" C   PRO A  34 "
            pdb=" CB  PRO A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  ILE A 761 "
            pdb=" N   ILE A 761 "
            pdb=" C   ILE A 761 "
            pdb=" CB  ILE A 761 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  ... (remaining 697 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  15 "    0.028 5.00e-02 4.00e+02   4.23e-02 2.86e+00
        pdb=" N   PRO B  16 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B  16 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B  16 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 712 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO A 713 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 713 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 713 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A  33 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A  34 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A  34 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  34 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 948
        2.78 -     3.31: 4419
        3.31 -     3.84: 7481
        3.84 -     4.37: 8784
        4.37 -     4.90: 14699
  Nonbonded interactions: 36331
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 806 "
            pdb=" OH  TYR A 821 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NH1 ARG A  11 "
            pdb=" OD1 ASP B  99 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" O   PRO A 756 "
            pdb=" OG  SER A 768 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" NH2 ARG A  11 "
            pdb=" OE1 GLU A  16 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" NE2 HIS A 839 "
            pdb=" OD2 ASP A 847 "
     model   vdw
     2.357 3.120
  ... (remaining 36326 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:             2.250
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.690
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4585  Z= 0.200
  Angle     :  0.542   7.096   6201  Z= 0.301
  Chirality :  0.044   0.169    700
  Planarity :  0.004   0.042    790
  Dihedral  : 13.673  81.517   1685
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.78 (0.35), residues: 552
  helix:  1.99 (0.31), residues: 289
  sheet:  1.00 (0.69), residues: 61
  loop :  0.13 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A   6 
 HIS   0.007   0.001   HIS A  33 
 PHE   0.013   0.002   PHE A 744 
 TYR   0.011   0.002   TYR A 725 
 ARG   0.002   0.000   ARG A 686 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11589 (  264)
  hydrogen bonds       : angle       5.33679 (  768)
  covalent geometry    : bond        0.00446 ( 4585)
  covalent geometry    : angle       0.54226 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7074 (mt-10)
REVERT: A  598 GLN cc_start: 0.8058 (mp-120) cc_final: 0.7788 (mm-40)
REVERT: A  602 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8065 (mtpp)
REVERT: A  642 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7654 (ttmm)
REVERT: A  661 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7639 (tmm-80)
REVERT: A  679 ASN cc_start: 0.7791 (m-40) cc_final: 0.7147 (m-40)
REVERT: A  696 LYS cc_start: 0.8158 (mttt) cc_final: 0.7949 (mttt)
REVERT: A  825 LEU cc_start: 0.8791 (mt) cc_final: 0.8560 (mp)
REVERT: A  855 LYS cc_start: 0.7823 (mtpt) cc_final: 0.7184 (mtpt)
REVERT: A  862 LYS cc_start: 0.8188 (tppt) cc_final: 0.7735 (tppt)
REVERT: A  881 ASP cc_start: 0.7609 (m-30) cc_final: 0.7285 (m-30)
REVERT: A  894 PHE cc_start: 0.8616 (t80) cc_final: 0.8137 (t80)
REVERT: A  911 GLN cc_start: 0.7991 (tp40) cc_final: 0.7463 (tp40)
REVERT: A  915 ASN cc_start: 0.8247 (m-40) cc_final: 0.7572 (m110)
REVERT: B  105 LEU cc_start: 0.8363 (mp) cc_final: 0.8097 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.2168
  time to fit residues: 38.3179
Evaluate side-chains
  139 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    0.3980
   chunk 43 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0060
   chunk 26 optimal weight:    0.2980
   chunk 32 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN
A 666 ASN
A 673 GLN
A 806 GLN
A 813 ASN
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 907 ASN
A 911 GLN
B   4 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.127330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.110718 restraints weight = 6576.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.22
r_work: 0.3327 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4585  Z= 0.163
  Angle     :  0.526   6.891   6201  Z= 0.280
  Chirality :  0.043   0.184    700
  Planarity :  0.004   0.042    790
  Dihedral  :  4.506  17.356    598
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 (0.35), residues: 552
  helix:  1.94 (0.30), residues: 296
  sheet:  0.86 (0.69), residues: 61
  loop :  0.22 (0.43), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 
 PHE   0.014   0.002   PHE A 779 
 TYR   0.008   0.001   TYR A 707 
 ARG   0.003   0.000   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04264 (  264)
  hydrogen bonds       : angle       4.64863 (  768)
  covalent geometry    : bond        0.00367 ( 4585)
  covalent geometry    : angle       0.52617 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7332 (mt-10)
REVERT: A  598 GLN cc_start: 0.8069 (mp-120) cc_final: 0.7860 (mm-40)
REVERT: A  602 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8378 (mtpp)
REVERT: A  642 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7678 (ttmm)
REVERT: A  673 GLN cc_start: 0.8494 (tp40) cc_final: 0.8276 (tp40)
REVERT: A  679 ASN cc_start: 0.7704 (m-40) cc_final: 0.7477 (m110)
REVERT: A  684 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7527 (mt-10)
REVERT: A  696 LYS cc_start: 0.8375 (mttt) cc_final: 0.8104 (mttt)
REVERT: A  702 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7839 (ttm110)
REVERT: A  825 LEU cc_start: 0.8944 (mt) cc_final: 0.8613 (mp)
REVERT: A  855 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7158 (mtpt)
REVERT: A  862 LYS cc_start: 0.8368 (tppt) cc_final: 0.7895 (tppt)
REVERT: A  881 ASP cc_start: 0.7789 (m-30) cc_final: 0.7419 (m-30)
REVERT: A  894 PHE cc_start: 0.8703 (t80) cc_final: 0.8302 (t80)
REVERT: B   34 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7857 (mtpt)
REVERT: B  105 LEU cc_start: 0.8468 (mp) cc_final: 0.8231 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2339
  time to fit residues: 37.8705
Evaluate side-chains
  131 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 10 optimal weight:    0.0970
   chunk 12 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.1980
   chunk 49 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 666 ASN
A 813 ASN
A 839 HIS
B   4 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.126472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.109917 restraints weight = 6616.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.22
r_work: 0.3313 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4585  Z= 0.193
  Angle     :  0.543   6.791   6201  Z= 0.290
  Chirality :  0.044   0.186    700
  Planarity :  0.004   0.042    790
  Dihedral  :  4.542  17.481    598
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 15.23 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.69 (0.35), residues: 552
  helix:  1.84 (0.30), residues: 296
  sheet:  0.76 (0.68), residues: 61
  loop :  0.22 (0.43), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A   6 
 HIS   0.007   0.001   HIS A  33 
 PHE   0.018   0.002   PHE A 779 
 TYR   0.011   0.001   TYR A 808 
 ARG   0.004   0.000   ARG A 661 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04256 (  264)
  hydrogen bonds       : angle       4.58416 (  768)
  covalent geometry    : bond        0.00437 ( 4585)
  covalent geometry    : angle       0.54287 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7351 (mt-10)
REVERT: A  598 GLN cc_start: 0.8051 (mp-120) cc_final: 0.7842 (mm-40)
REVERT: A  642 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7668 (ttmm)
REVERT: A  651 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7078 (mt-10)
REVERT: A  684 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7566 (mt-10)
REVERT: A  696 LYS cc_start: 0.8447 (mttt) cc_final: 0.8168 (mttt)
REVERT: A  702 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7853 (ttm110)
REVERT: A  806 GLN cc_start: 0.7827 (tp40) cc_final: 0.7427 (tp40)
REVERT: A  855 LYS cc_start: 0.7598 (mtpt) cc_final: 0.7261 (mtpt)
REVERT: A  862 LYS cc_start: 0.8406 (tppt) cc_final: 0.7902 (tppt)
REVERT: A  881 ASP cc_start: 0.7809 (m-30) cc_final: 0.7447 (m-30)
REVERT: A  894 PHE cc_start: 0.8703 (t80) cc_final: 0.8326 (t80)
REVERT: B  105 LEU cc_start: 0.8472 (mp) cc_final: 0.8217 (mm)
REVERT: B  168 VAL cc_start: 0.8547 (t) cc_final: 0.8074 (m)
  outliers start: 4
  outliers final: 2
  residues processed: 139
  average time/residue: 0.2210
  time to fit residues: 36.7681
Evaluate side-chains
  141 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 138
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  893 SER
Chi-restraints excluded: chain B residue  172 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 10 optimal weight:    0.4980
   chunk 9 optimal weight:    0.2980
   chunk 3 optimal weight:    0.2980
   chunk 21 optimal weight:    0.0980
   chunk 40 optimal weight:    0.8980
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
A 673 GLN
** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
B   4 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.127906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.111380 restraints weight = 6645.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 2.23
r_work: 0.3343 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4585  Z= 0.142
  Angle     :  0.513   6.303   6201  Z= 0.272
  Chirality :  0.042   0.172    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.413  17.030    598
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 16.63 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.81 (0.36), residues: 552
  helix:  1.95 (0.30), residues: 297
  sheet:  0.71 (0.66), residues: 61
  loop :  0.29 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  97 
 HIS   0.004   0.001   HIS A  33 
 PHE   0.012   0.001   PHE A 779 
 TYR   0.008   0.001   TYR A 808 
 ARG   0.004   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  264)
  hydrogen bonds       : angle       4.44742 (  768)
  covalent geometry    : bond        0.00319 ( 4585)
  covalent geometry    : angle       0.51345 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 136
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 GLN cc_start: 0.7991 (mp-120) cc_final: 0.7784 (mm-40)
REVERT: A  642 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7713 (ttmm)
REVERT: A  679 ASN cc_start: 0.7687 (m-40) cc_final: 0.7464 (m110)
REVERT: A  684 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7408 (mt-10)
REVERT: A  696 LYS cc_start: 0.8418 (mttt) cc_final: 0.8146 (mttt)
REVERT: A  702 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7818 (ttm110)
REVERT: A  765 MET cc_start: 0.7966 (mmm) cc_final: 0.7101 (mmm)
REVERT: A  804 VAL cc_start: 0.8532 (t) cc_final: 0.8304 (p)
REVERT: A  855 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7231 (mtpt)
REVERT: A  862 LYS cc_start: 0.8395 (tppt) cc_final: 0.7912 (tppt)
REVERT: A  881 ASP cc_start: 0.7814 (m-30) cc_final: 0.7444 (m-30)
REVERT: A  888 SER cc_start: 0.8328 (t) cc_final: 0.8125 (p)
REVERT: A  894 PHE cc_start: 0.8689 (t80) cc_final: 0.8322 (t80)
REVERT: B  105 LEU cc_start: 0.8501 (mp) cc_final: 0.8248 (mm)
REVERT: B  168 VAL cc_start: 0.8570 (t) cc_final: 0.8086 (m)
  outliers start: 4
  outliers final: 3
  residues processed: 136
  average time/residue: 0.2297
  time to fit residues: 37.0526
Evaluate side-chains
  137 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain B residue  172 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 47 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0570
   chunk 2 optimal weight:    0.9980
   chunk 39 optimal weight:    0.3980
   chunk 13 optimal weight:    0.3980
   chunk 21 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.3298

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

Flipped N/Q/H residues before XYZ refinement:
A 666 ASN
A 673 GLN
A 789 HIS
** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.127905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.111505 restraints weight = 6752.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.24
r_work: 0.3337 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4585  Z= 0.144
  Angle     :  0.504   6.289   6201  Z= 0.272
  Chirality :  0.042   0.144    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.376  17.398    598
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 17.23 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.82 (0.36), residues: 552
  helix:  1.93 (0.30), residues: 297
  sheet:  0.76 (0.63), residues: 71
  loop :  0.32 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 
 PHE   0.011   0.001   PHE A 779 
 TYR   0.010   0.001   TYR A 808 
 ARG   0.003   0.000   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  264)
  hydrogen bonds       : angle       4.42317 (  768)
  covalent geometry    : bond        0.00326 ( 4585)
  covalent geometry    : angle       0.50416 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 133
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8281 (mmm) cc_final: 0.7949 (mmm)
REVERT: A  642 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7832 (ttmm)
REVERT: A  651 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7096 (mt-10)
REVERT: A  679 ASN cc_start: 0.7707 (m-40) cc_final: 0.7475 (m110)
REVERT: A  684 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7418 (mt-10)
REVERT: A  696 LYS cc_start: 0.8417 (mttt) cc_final: 0.8160 (mttt)
REVERT: A  702 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7828 (ttm110)
REVERT: A  765 MET cc_start: 0.7952 (mmm) cc_final: 0.7094 (mmm)
REVERT: A  804 VAL cc_start: 0.8520 (t) cc_final: 0.8284 (p)
REVERT: A  806 GLN cc_start: 0.7887 (tp40) cc_final: 0.7397 (tp-100)
REVERT: A  862 LYS cc_start: 0.8392 (tppt) cc_final: 0.7913 (tppt)
REVERT: A  881 ASP cc_start: 0.7862 (m-30) cc_final: 0.7491 (m-30)
REVERT: A  888 SER cc_start: 0.8319 (t) cc_final: 0.8117 (p)
REVERT: A  894 PHE cc_start: 0.8676 (t80) cc_final: 0.8310 (t80)
REVERT: B  105 LEU cc_start: 0.8491 (mp) cc_final: 0.8244 (mm)
REVERT: B  168 VAL cc_start: 0.8576 (t) cc_final: 0.8105 (m)
  outliers start: 5
  outliers final: 3
  residues processed: 134
  average time/residue: 0.2181
  time to fit residues: 34.6305
Evaluate side-chains
  136 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LYS
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain B residue  172 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 19 optimal weight:    0.1980
   chunk 18 optimal weight:    0.1980
   chunk 21 optimal weight:    0.0980
   chunk 2 optimal weight:    0.8980
   chunk 13 optimal weight:    0.1980
   chunk 46 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.2780

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

Flipped N/Q/H residues before XYZ refinement:
A 598 GLN
A 666 ASN
A 673 GLN
** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.128103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.111871 restraints weight = 6657.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.24
r_work: 0.3333 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4585  Z= 0.132
  Angle     :  0.509   7.301   6201  Z= 0.269
  Chirality :  0.042   0.137    700
  Planarity :  0.004   0.042    790
  Dihedral  :  4.321  17.377    598
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.83 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.92 (0.36), residues: 552
  helix:  2.00 (0.30), residues: 297
  sheet:  0.79 (0.63), residues: 71
  loop :  0.38 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A   6 
 HIS   0.004   0.001   HIS A  33 
 PHE   0.009   0.001   PHE A 779 
 TYR   0.017   0.001   TYR A 725 
 ARG   0.003   0.000   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03571 (  264)
  hydrogen bonds       : angle       4.37071 (  768)
  covalent geometry    : bond        0.00296 ( 4585)
  covalent geometry    : angle       0.50856 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8297 (mmm) cc_final: 0.8014 (mmm)
REVERT: A  642 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7761 (ttmm)
REVERT: A  651 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7123 (mt-10)
REVERT: A  679 ASN cc_start: 0.7784 (m-40) cc_final: 0.7559 (m110)
REVERT: A  684 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7307 (mt-10)
REVERT: A  696 LYS cc_start: 0.8408 (mttt) cc_final: 0.8142 (mttt)
REVERT: A  702 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7811 (ttm110)
REVERT: A  765 MET cc_start: 0.7926 (mmm) cc_final: 0.7117 (mmm)
REVERT: A  804 VAL cc_start: 0.8490 (t) cc_final: 0.8257 (p)
REVERT: A  806 GLN cc_start: 0.7871 (tp40) cc_final: 0.7461 (tp-100)
REVERT: A  862 LYS cc_start: 0.8363 (tppt) cc_final: 0.7914 (tppt)
REVERT: A  894 PHE cc_start: 0.8656 (t80) cc_final: 0.8242 (t80)
REVERT: B   34 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7633 (mtpt)
REVERT: B  105 LEU cc_start: 0.8458 (mp) cc_final: 0.8215 (mm)
REVERT: B  168 VAL cc_start: 0.8567 (t) cc_final: 0.8094 (m)
  outliers start: 10
  outliers final: 5
  residues processed: 135
  average time/residue: 0.2324
  time to fit residues: 37.2649
Evaluate side-chains
  133 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain B residue  172 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    0.3980
   chunk 51 optimal weight:    0.0170
   chunk 9 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   chunk 29 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.3818

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

Flipped N/Q/H residues before XYZ refinement:
A 598 GLN
A 666 ASN
** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.127338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.111056 restraints weight = 6717.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.25
r_work: 0.3323 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4585  Z= 0.161
  Angle     :  0.542   8.304   6201  Z= 0.286
  Chirality :  0.043   0.143    700
  Planarity :  0.004   0.042    790
  Dihedral  :  4.371  18.103    598
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.23 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 (0.36), residues: 552
  helix:  1.94 (0.30), residues: 297
  sheet:  0.80 (0.63), residues: 71
  loop :  0.32 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A   6 
 HIS   0.006   0.001   HIS A  33 
 PHE   0.012   0.001   PHE A 779 
 TYR   0.018   0.001   TYR A 725 
 ARG   0.004   0.000   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03773 (  264)
  hydrogen bonds       : angle       4.40127 (  768)
  covalent geometry    : bond        0.00365 ( 4585)
  covalent geometry    : angle       0.54166 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8286 (mmm) cc_final: 0.7991 (mmm)
REVERT: A  651 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7193 (mt-10)
REVERT: A  679 ASN cc_start: 0.7750 (m-40) cc_final: 0.7521 (m110)
REVERT: A  684 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7318 (mt-10)
REVERT: A  696 LYS cc_start: 0.8423 (mttt) cc_final: 0.8161 (mttt)
REVERT: A  702 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.7843 (ttm110)
REVERT: A  765 MET cc_start: 0.7892 (mmm) cc_final: 0.7413 (mpp)
REVERT: A  806 GLN cc_start: 0.7884 (tp40) cc_final: 0.7476 (tp-100)
REVERT: A  862 LYS cc_start: 0.8329 (tppt) cc_final: 0.7907 (tppt)
REVERT: A  894 PHE cc_start: 0.8658 (t80) cc_final: 0.8279 (t80)
REVERT: B   34 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7649 (mtpt)
REVERT: B  105 LEU cc_start: 0.8503 (mp) cc_final: 0.8259 (mm)
REVERT: B  168 VAL cc_start: 0.8577 (t) cc_final: 0.8107 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 129
  average time/residue: 0.2395
  time to fit residues: 36.4227
Evaluate side-chains
  132 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  172 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 598 GLN
A 666 ASN
A 673 GLN
A 813 ASN
** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.124691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.108719 restraints weight = 6733.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.20
r_work: 0.3287 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   4585  Z= 0.286
  Angle     :  0.621   7.688   6201  Z= 0.329
  Chirality :  0.047   0.154    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.710  20.205    598
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.23 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.44 (0.35), residues: 552
  helix:  1.65 (0.29), residues: 296
  sheet:  0.69 (0.68), residues: 59
  loop :  0.08 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A   6 
 HIS   0.011   0.002   HIS A  33 
 PHE   0.019   0.002   PHE A 779 
 TYR   0.025   0.002   TYR A 725 
 ARG   0.004   0.001   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04619 (  264)
  hydrogen bonds       : angle       4.63095 (  768)
  covalent geometry    : bond        0.00645 ( 4585)
  covalent geometry    : angle       0.62137 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8204 (mmm) cc_final: 0.7842 (mmm)
REVERT: A  684 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7538 (mt-10)
REVERT: A  765 MET cc_start: 0.7915 (mmm) cc_final: 0.7426 (mpp)
REVERT: A  859 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7325 (mm-30)
REVERT: A  862 LYS cc_start: 0.8377 (tppt) cc_final: 0.7977 (tppt)
REVERT: A  894 PHE cc_start: 0.8728 (t80) cc_final: 0.8303 (t80)
REVERT: B   34 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7715 (mtpt)
REVERT: B  105 LEU cc_start: 0.8510 (mp) cc_final: 0.8261 (mm)
REVERT: B  168 VAL cc_start: 0.8628 (t) cc_final: 0.8175 (m)
  outliers start: 10
  outliers final: 7
  residues processed: 136
  average time/residue: 0.2281
  time to fit residues: 36.8195
Evaluate side-chains
  139 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  893 SER
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  172 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    0.1980
   chunk 54 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 18 optimal weight:    0.2980
   chunk 16 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0570
   chunk 50 optimal weight:    0.4980
   overall best weight:    0.3298

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

Flipped N/Q/H residues before XYZ refinement:
A 598 GLN
A 666 ASN
A 673 GLN
A 813 ASN
** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.127284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.111189 restraints weight = 6708.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.23
r_work: 0.3326 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4585  Z= 0.149
  Angle     :  0.545   6.827   6201  Z= 0.286
  Chirality :  0.042   0.140    700
  Planarity :  0.004   0.039    790
  Dihedral  :  4.512  20.033    598
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 18.64 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.73 (0.36), residues: 552
  helix:  1.89 (0.30), residues: 297
  sheet:  0.88 (0.64), residues: 69
  loop :  0.13 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  97 
 HIS   0.004   0.001   HIS A  33 
 PHE   0.011   0.001   PHE A 779 
 TYR   0.019   0.001   TYR A 725 
 ARG   0.006   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03760 (  264)
  hydrogen bonds       : angle       4.48157 (  768)
  covalent geometry    : bond        0.00338 ( 4585)
  covalent geometry    : angle       0.54474 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8221 (mmm) cc_final: 0.7925 (mmm)
REVERT: A  679 ASN cc_start: 0.7739 (m-40) cc_final: 0.7170 (m-40)
REVERT: A  684 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7401 (mt-10)
REVERT: A  702 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7848 (ttm110)
REVERT: A  765 MET cc_start: 0.7936 (mmm) cc_final: 0.7096 (mmm)
REVERT: A  862 LYS cc_start: 0.8363 (tppt) cc_final: 0.7928 (tppt)
REVERT: A  894 PHE cc_start: 0.8677 (t80) cc_final: 0.8278 (t80)
REVERT: B   34 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7667 (mtpt)
REVERT: B  105 LEU cc_start: 0.8486 (mp) cc_final: 0.8246 (mm)
REVERT: B  168 VAL cc_start: 0.8582 (t) cc_final: 0.8095 (m)
  outliers start: 7
  outliers final: 6
  residues processed: 132
  average time/residue: 0.2294
  time to fit residues: 36.2122
Evaluate side-chains
  132 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain A residue  893 SER
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  172 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 17 optimal weight:    0.0270
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   chunk 42 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0470
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.3136

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

Flipped N/Q/H residues before XYZ refinement:
A 666 ASN
A 673 GLN
A 813 ASN
** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.127863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.111608 restraints weight = 6745.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.25
r_work: 0.3331 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4585  Z= 0.147
  Angle     :  0.541   6.777   6201  Z= 0.286
  Chirality :  0.042   0.142    700
  Planarity :  0.004   0.037    790
  Dihedral  :  4.449  20.627    598
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.04 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.85 (0.36), residues: 552
  helix:  1.97 (0.30), residues: 297
  sheet:  1.03 (0.65), residues: 69
  loop :  0.19 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 
 PHE   0.013   0.001   PHE B 154 
 TYR   0.017   0.001   TYR A 725 
 ARG   0.005   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  264)
  hydrogen bonds       : angle       4.41734 (  768)
  covalent geometry    : bond        0.00336 ( 4585)
  covalent geometry    : angle       0.54119 ( 6201)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8252 (mmm) cc_final: 0.7959 (mmm)
REVERT: A  642 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7707 (mtpp)
REVERT: A  679 ASN cc_start: 0.7736 (m-40) cc_final: 0.7166 (m110)
REVERT: A  684 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7397 (mt-10)
REVERT: A  702 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7823 (ttm110)
REVERT: A  765 MET cc_start: 0.7970 (mmm) cc_final: 0.7108 (mmm)
REVERT: A  806 GLN cc_start: 0.7945 (tp40) cc_final: 0.7676 (tp40)
REVERT: A  862 LYS cc_start: 0.8342 (tppt) cc_final: 0.7921 (tppt)
REVERT: A  894 PHE cc_start: 0.8679 (t80) cc_final: 0.8259 (t80)
REVERT: B   34 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7546 (mtpt)
REVERT: B  105 LEU cc_start: 0.8483 (mp) cc_final: 0.8243 (mm)
REVERT: B  129 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7595 (mm-30)
REVERT: B  168 VAL cc_start: 0.8600 (t) cc_final: 0.8108 (m)
  outliers start: 7
  outliers final: 6
  residues processed: 134
  average time/residue: 0.2358
  time to fit residues: 37.5588
Evaluate side-chains
  136 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 LYS
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain A residue  893 SER
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  172 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 12 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0070
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.3998

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

Flipped N/Q/H residues before XYZ refinement:
A 666 ASN
A 673 GLN
A 813 ASN
** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.127306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.111014 restraints weight = 6666.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.22
r_work: 0.3329 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4585  Z= 0.168
  Angle     :  0.554   6.797   6201  Z= 0.292
  Chirality :  0.042   0.148    700
  Planarity :  0.004   0.036    790
  Dihedral  :  4.485  21.359    598
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 18.84 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.85 (0.36), residues: 552
  helix:  1.97 (0.30), residues: 297
  sheet:  0.98 (0.64), residues: 69
  loop :  0.20 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A   6 
 HIS   0.006   0.001   HIS A  33 
 PHE   0.013   0.001   PHE B 154 
 TYR   0.018   0.001   TYR A 725 
 ARG   0.005   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03818 (  264)
  hydrogen bonds       : angle       4.43269 (  768)
  covalent geometry    : bond        0.00385 ( 4585)
  covalent geometry    : angle       0.55367 ( 6201)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2774.72 seconds
wall clock time: 49 minutes 16.81 seconds (2956.81 seconds total)