Starting phenix.real_space_refine
on Thu Mar  6 02:16:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sym_40884/03_2025/8sym_40884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sym_40884/03_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_40884/03_2025/8sym_40884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sym_40884/03_2025/8sym_40884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sym_40884/03_2025/8sym_40884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sym_40884/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.44, per 1000 atoms: 0.77
  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: 1.17
  Conformation dependent library (CDL) restraints added in 547.6 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: 0.52
  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: 1.17

  Time building geometry restraints manager: 1.39 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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     15.500
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.800
-------------------------------------------------------------------------------
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= 0.287
  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 

*********************** 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  : 0.564 
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: 0.2399
  time to fit residues: 42.5363
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  : 0.579 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 43 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0060
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.3683 r_free = 0.3683 target = 0.126469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.109886 restraints weight = 6587.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.21
r_work: 0.3318 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4585  Z= 0.278
  Angle     :  0.545   7.157   6201  Z= 0.289
  Chirality :  0.044   0.188    700
  Planarity :  0.004   0.042    790
  Dihedral  :  4.576  17.905    598
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  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:  1.70 (0.35), residues: 552
  helix:  1.88 (0.30), residues: 295
  sheet:  0.85 (0.69), residues: 61
  loop :  0.16 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A   6 
 HIS   0.007   0.001   HIS A  33 
 PHE   0.018   0.002   PHE A 779 
 TYR   0.010   0.001   TYR A 707 
 ARG   0.003   0.000   ARG A 680 

*********************** 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  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7361 (mt-10)
REVERT: A  598 GLN cc_start: 0.8097 (mp-120) cc_final: 0.7867 (mm-40)
REVERT: A  602 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8383 (mtpp)
REVERT: A  642 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7696 (ttmm)
REVERT: A  679 ASN cc_start: 0.7702 (m-40) cc_final: 0.7457 (m110)
REVERT: A  684 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7649 (mt-10)
REVERT: A  696 LYS cc_start: 0.8435 (mttt) cc_final: 0.8164 (mttt)
REVERT: A  825 LEU cc_start: 0.8960 (mt) cc_final: 0.8635 (mp)
REVERT: A  855 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7168 (mtpt)
REVERT: A  862 LYS cc_start: 0.8390 (tppt) cc_final: 0.7918 (tppt)
REVERT: A  881 ASP cc_start: 0.7789 (m-30) cc_final: 0.7419 (m-30)
REVERT: A  894 PHE cc_start: 0.8725 (t80) cc_final: 0.8315 (t80)
REVERT: B   34 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7876 (mtpt)
REVERT: B  105 LEU cc_start: 0.8426 (mp) cc_final: 0.8184 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.3220
  time to fit residues: 52.8257
Evaluate side-chains
  134 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 12 optimal weight:    0.1980
   chunk 4 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.3980
   chunk 49 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.126531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.110178 restraints weight = 6610.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.20
r_work: 0.3319 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4585  Z= 0.270
  Angle     :  0.541   6.795   6201  Z= 0.289
  Chirality :  0.044   0.183    700
  Planarity :  0.004   0.042    790
  Dihedral  :  4.572  18.275    598
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 15.23 %
    Favored  : 83.77 %
  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:  1.66 (0.35), residues: 552
  helix:  1.84 (0.30), residues: 296
  sheet:  0.74 (0.68), residues: 61
  loop :  0.17 (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 707 
 ARG   0.003   0.000   ARG A 680 

*********************** 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
  146 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 141
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7374 (mt-10)
REVERT: A  642 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7663 (ttmm)
REVERT: A  651 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7088 (mt-10)
REVERT: A  679 ASN cc_start: 0.7681 (m-40) cc_final: 0.7403 (m110)
REVERT: A  684 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7570 (mt-10)
REVERT: A  696 LYS cc_start: 0.8438 (mttt) cc_final: 0.8165 (mttt)
REVERT: A  702 ARG cc_start: 0.8052 (mtt-85) cc_final: 0.7843 (ttm110)
REVERT: A  806 GLN cc_start: 0.7835 (tp40) cc_final: 0.7450 (tp40)
REVERT: A  855 LYS cc_start: 0.7592 (mtpt) cc_final: 0.7257 (mtpt)
REVERT: A  862 LYS cc_start: 0.8422 (tppt) cc_final: 0.7907 (tppt)
REVERT: A  881 ASP cc_start: 0.7830 (m-30) cc_final: 0.7469 (m-30)
REVERT: A  894 PHE cc_start: 0.8708 (t80) cc_final: 0.8328 (t80)
REVERT: B  105 LEU cc_start: 0.8510 (mp) cc_final: 0.8257 (mm)
REVERT: B  168 VAL cc_start: 0.8543 (t) cc_final: 0.8077 (m)
  outliers start: 5
  outliers final: 3
  residues processed: 141
  average time/residue: 0.3486
  time to fit residues: 58.3985
Evaluate side-chains
  138 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain B residue  171 LEU
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:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0870
   chunk 21 optimal weight:    0.7980
   chunk 40 optimal weight:    0.4980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 833 GLN ** 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 = 0.3679 r_free = 0.3679 target = 0.126111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.109645 restraints weight = 6671.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.22
r_work: 0.3315 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4585  Z= 0.269
  Angle     :  0.542   6.826   6201  Z= 0.288
  Chirality :  0.043   0.171    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.541  18.528    598
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.63 %
    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:  1.65 (0.35), residues: 552
  helix:  1.82 (0.30), residues: 296
  sheet:  0.69 (0.69), residues: 61
  loop :  0.20 (0.44), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  97 
 HIS   0.007   0.001   HIS A  33 
 PHE   0.015   0.001   PHE A 779 
 TYR   0.011   0.001   TYR A 808 
 ARG   0.005   0.001   ARG A 661 

*********************** 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
  148 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  642 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7761 (ttmm)
REVERT: A  651 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7151 (mt-10)
REVERT: A  679 ASN cc_start: 0.7694 (m-40) cc_final: 0.7422 (m110)
REVERT: A  684 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7534 (mt-10)
REVERT: A  696 LYS cc_start: 0.8477 (mttt) cc_final: 0.8206 (mttt)
REVERT: A  702 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7891 (ttm110)
REVERT: A  765 MET cc_start: 0.7948 (mmm) cc_final: 0.7065 (mmm)
REVERT: A  855 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7284 (mtpt)
REVERT: A  862 LYS cc_start: 0.8397 (tppt) cc_final: 0.7941 (tppt)
REVERT: A  881 ASP cc_start: 0.7868 (m-30) cc_final: 0.7499 (m-30)
REVERT: A  888 SER cc_start: 0.8342 (t) cc_final: 0.8139 (p)
REVERT: A  894 PHE cc_start: 0.8704 (t80) cc_final: 0.8290 (t80)
REVERT: B  105 LEU cc_start: 0.8528 (mp) cc_final: 0.8268 (mm)
REVERT: B  168 VAL cc_start: 0.8579 (t) cc_final: 0.8101 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 140
  average time/residue: 0.2637
  time to fit residues: 43.9951
Evaluate side-chains
  144 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
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  794 VAL
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain A residue  893 SER
Chi-restraints excluded: chain B residue  171 LEU
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:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 50 optimal weight:    0.2980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0970
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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
B   4 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.127220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.110701 restraints weight = 6783.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.24
r_work: 0.3331 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1642

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= 0.220
  Angle     :  0.516   6.664   6201  Z= 0.277
  Chirality :  0.042   0.150    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.472  18.385    598
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 18.24 %
    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:  1.70 (0.36), residues: 552
  helix:  1.84 (0.30), residues: 297
  sheet:  0.75 (0.64), residues: 71
  loop :  0.23 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  97 
 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   0.004   0.000   ARG A 661 

*********************** 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
  137 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8340 (mmm) cc_final: 0.8118 (mmm)
REVERT: A  642 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7685 (ttmm)
REVERT: A  664 PHE cc_start: 0.8141 (m-80) cc_final: 0.7623 (m-80)
REVERT: A  679 ASN cc_start: 0.7686 (m-40) cc_final: 0.7446 (m110)
REVERT: A  684 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7438 (mt-10)
REVERT: A  696 LYS cc_start: 0.8425 (mttt) cc_final: 0.8165 (mttt)
REVERT: A  702 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7835 (ttm110)
REVERT: A  765 MET cc_start: 0.7948 (mmm) cc_final: 0.7091 (mmm)
REVERT: A  804 VAL cc_start: 0.8521 (t) cc_final: 0.8284 (p)
REVERT: A  806 GLN cc_start: 0.7871 (tp40) cc_final: 0.7364 (tp-100)
REVERT: A  862 LYS cc_start: 0.8402 (tppt) cc_final: 0.7936 (tppt)
REVERT: A  888 SER cc_start: 0.8311 (t) cc_final: 0.8109 (p)
REVERT: A  894 PHE cc_start: 0.8674 (t80) cc_final: 0.8293 (t80)
REVERT: B  105 LEU cc_start: 0.8520 (mp) cc_final: 0.8269 (mm)
REVERT: B  168 VAL cc_start: 0.8579 (t) cc_final: 0.8098 (m)
  outliers start: 5
  outliers final: 5
  residues processed: 132
  average time/residue: 0.2300
  time to fit residues: 35.9068
Evaluate side-chains
  135 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  773 LEU
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  893 SER
Chi-restraints excluded: chain B residue  171 LEU
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:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0570
   chunk 21 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 46 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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 789 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 = 0.3669 r_free = 0.3669 target = 0.126187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.110032 restraints weight = 6684.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.22
r_work: 0.3309 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.1726

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= 0.268
  Angle     :  0.545   7.696   6201  Z= 0.291
  Chirality :  0.043   0.137    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.512  19.421    598
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.64 %
    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:  1.67 (0.36), residues: 552
  helix:  1.81 (0.30), residues: 297
  sheet:  0.69 (0.64), residues: 71
  loop :  0.24 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A   6 
 HIS   0.007   0.001   HIS A  33 
 PHE   0.014   0.001   PHE A 779 
 TYR   0.013   0.001   TYR A 808 
 ARG   0.004   0.001   ARG A 695 

*********************** 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
  143 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8289 (mmm) cc_final: 0.7954 (mmm)
REVERT: A  642 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7724 (ttmm)
REVERT: A  664 PHE cc_start: 0.8115 (m-80) cc_final: 0.7643 (m-80)
REVERT: A  679 ASN cc_start: 0.7757 (m-40) cc_final: 0.7516 (m110)
REVERT: A  684 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7454 (mt-10)
REVERT: A  696 LYS cc_start: 0.8443 (mttt) cc_final: 0.8193 (mttt)
REVERT: A  702 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7840 (ttm110)
REVERT: A  765 MET cc_start: 0.7900 (mmm) cc_final: 0.6974 (mmm)
REVERT: A  806 GLN cc_start: 0.7872 (tp40) cc_final: 0.7457 (tp40)
REVERT: A  862 LYS cc_start: 0.8402 (tppt) cc_final: 0.7950 (tppt)
REVERT: A  894 PHE cc_start: 0.8685 (t80) cc_final: 0.8277 (t80)
REVERT: B   34 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7695 (mtpt)
REVERT: B  105 LEU cc_start: 0.8482 (mp) cc_final: 0.8220 (mm)
REVERT: B  168 VAL cc_start: 0.8585 (t) cc_final: 0.8118 (m)
  outliers start: 12
  outliers final: 8
  residues processed: 135
  average time/residue: 0.2891
  time to fit residues: 45.8295
Evaluate side-chains
  137 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  773 LEU
Chi-restraints excluded: chain A residue  794 VAL
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  171 LEU
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:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 39 optimal weight:    0.4980
   chunk 51 optimal weight:    0.0980
   chunk 9 optimal weight:    0.0370
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.3458

-------------------------------------------------------------------------------
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
B   4 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.127218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.111146 restraints weight = 6731.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.22
r_work: 0.3322 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4585  Z= 0.215
  Angle     :  0.521   6.428   6201  Z= 0.278
  Chirality :  0.042   0.137    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.450  19.301    598
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.84 %
    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:  1.77 (0.36), residues: 552
  helix:  1.92 (0.30), residues: 297
  sheet:  0.71 (0.64), residues: 71
  loop :  0.23 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 
 PHE   0.010   0.001   PHE B 154 
 TYR   0.012   0.001   TYR A 808 
 ARG   0.004   0.001   ARG A 680 

*********************** 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
  140 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8268 (mmm) cc_final: 0.7904 (mmm)
REVERT: A  664 PHE cc_start: 0.8036 (m-80) cc_final: 0.7615 (m-80)
REVERT: A  679 ASN cc_start: 0.7771 (m-40) cc_final: 0.7547 (m110)
REVERT: A  684 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7385 (mt-10)
REVERT: A  696 LYS cc_start: 0.8438 (mttt) cc_final: 0.8173 (mttt)
REVERT: A  702 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7837 (ttm110)
REVERT: A  765 MET cc_start: 0.7876 (mmm) cc_final: 0.7401 (mpp)
REVERT: A  806 GLN cc_start: 0.7920 (tp40) cc_final: 0.7507 (tp40)
REVERT: A  862 LYS cc_start: 0.8349 (tppt) cc_final: 0.7925 (tppt)
REVERT: A  894 PHE cc_start: 0.8653 (t80) cc_final: 0.8221 (t80)
REVERT: B   34 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7655 (mtpt)
REVERT: B  105 LEU cc_start: 0.8471 (mp) cc_final: 0.8215 (mm)
REVERT: B  168 VAL cc_start: 0.8573 (t) cc_final: 0.8100 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 132
  average time/residue: 0.2413
  time to fit residues: 37.8758
Evaluate side-chains
  136 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LYS
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  773 LEU
Chi-restraints excluded: chain A residue  794 VAL
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  171 LEU
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:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0980
   chunk 36 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 34 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   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 666 ASN
A 673 GLN
B   4 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.125809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.109554 restraints weight = 6716.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.22
r_work: 0.3296 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4585  Z= 0.315
  Angle     :  0.577   7.902   6201  Z= 0.303
  Chirality :  0.044   0.147    700
  Planarity :  0.004   0.036    790
  Dihedral  :  4.588  20.518    598
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.24 %
    Favored  : 79.16 %
  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:  1.62 (0.36), residues: 552
  helix:  1.78 (0.30), residues: 297
  sheet:  0.77 (0.66), residues: 69
  loop :  0.15 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A   6 
 HIS   0.008   0.001   HIS A  33 
 PHE   0.013   0.002   PHE A 779 
 TYR   0.013   0.001   TYR A 808 
 ARG   0.004   0.001   ARG A 680 

*********************** 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
  145 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8243 (mmm) cc_final: 0.7846 (mmm)
REVERT: A  618 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8260 (t-90)
REVERT: A  664 PHE cc_start: 0.8102 (m-80) cc_final: 0.7613 (m-80)
REVERT: A  679 ASN cc_start: 0.7804 (m-40) cc_final: 0.7577 (m110)
REVERT: A  684 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7499 (mt-10)
REVERT: A  702 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7828 (ttm110)
REVERT: A  765 MET cc_start: 0.7909 (mmm) cc_final: 0.7403 (mpp)
REVERT: A  859 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7369 (mm-30)
REVERT: A  862 LYS cc_start: 0.8375 (tppt) cc_final: 0.7938 (tppt)
REVERT: A  894 PHE cc_start: 0.8690 (t80) cc_final: 0.8296 (t80)
REVERT: B   34 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7703 (mtpt)
REVERT: B  105 LEU cc_start: 0.8496 (mp) cc_final: 0.8238 (mm)
REVERT: B  168 VAL cc_start: 0.8616 (t) cc_final: 0.8164 (m)
  outliers start: 13
  outliers final: 11
  residues processed: 137
  average time/residue: 0.2324
  time to fit residues: 37.8204
Evaluate side-chains
  142 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LYS
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  618 HIS
Chi-restraints excluded: chain A residue  773 LEU
Chi-restraints excluded: chain A residue  794 VAL
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  171 LEU
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:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0980
   chunk 54 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0270
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.3438

-------------------------------------------------------------------------------
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
B   4 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.127164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.110932 restraints weight = 6700.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.23
r_work: 0.3323 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4585  Z= 0.223
  Angle     :  0.552   7.728   6201  Z= 0.290
  Chirality :  0.042   0.139    700
  Planarity :  0.004   0.038    790
  Dihedral  :  4.482  20.729    598
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.84 %
    Favored  : 78.76 %
  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:  1.77 (0.36), residues: 552
  helix:  1.92 (0.30), residues: 297
  sheet:  0.78 (0.65), residues: 69
  loop :  0.20 (0.45), residues: 186

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 656 
 TYR   0.012   0.001   TYR A 808 
 ARG   0.004   0.000   ARG A 680 

*********************** 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
  141 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8253 (mmm) cc_final: 0.7881 (mmm)
REVERT: A  664 PHE cc_start: 0.8057 (m-80) cc_final: 0.7592 (m-80)
REVERT: A  679 ASN cc_start: 0.7782 (m-40) cc_final: 0.7556 (m110)
REVERT: A  684 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7389 (mt-10)
REVERT: A  702 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7820 (ttm110)
REVERT: A  765 MET cc_start: 0.7939 (mmm) cc_final: 0.7068 (mmm)
REVERT: A  806 GLN cc_start: 0.7953 (tp40) cc_final: 0.7681 (tp40)
REVERT: A  862 LYS cc_start: 0.8363 (tppt) cc_final: 0.7937 (tppt)
REVERT: A  894 PHE cc_start: 0.8678 (t80) cc_final: 0.8287 (t80)
REVERT: B   34 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7703 (mtpt)
REVERT: B  105 LEU cc_start: 0.8466 (mp) cc_final: 0.8213 (mm)
REVERT: B  168 VAL cc_start: 0.8574 (t) cc_final: 0.8113 (m)
  outliers start: 12
  outliers final: 12
  residues processed: 133
  average time/residue: 0.2459
  time to fit residues: 38.7100
Evaluate side-chains
  140 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LYS
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  773 LEU
Chi-restraints excluded: chain A residue  794 VAL
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  134 ILE
Chi-restraints excluded: chain B residue  171 LEU
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:    0.2980
   chunk 37 optimal weight:    0.6980
   chunk 35 optimal weight:    0.2980
   chunk 16 optimal weight:    0.1980
   chunk 17 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   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 666 ASN
A 673 GLN
B   4 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.126923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.110648 restraints weight = 6739.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.23
r_work: 0.3313 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4585  Z= 0.242
  Angle     :  0.559   7.552   6201  Z= 0.293
  Chirality :  0.043   0.145    700
  Planarity :  0.004   0.037    790
  Dihedral  :  4.471  21.358    598
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.04 %
    Favored  : 78.96 %
  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:  1.77 (0.36), residues: 552
  helix:  1.92 (0.30), residues: 297
  sheet:  0.80 (0.65), residues: 69
  loop :  0.22 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A   6 
 HIS   0.006   0.001   HIS A  33 
 PHE   0.011   0.001   PHE B 154 
 TYR   0.014   0.001   TYR A 808 
 ARG   0.006   0.001   ARG A 695 

********************** 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
  140 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8255 (mmm) cc_final: 0.7872 (mmm)
REVERT: A  664 PHE cc_start: 0.8060 (m-80) cc_final: 0.7607 (m-80)
REVERT: A  679 ASN cc_start: 0.7782 (m-40) cc_final: 0.7554 (m110)
REVERT: A  684 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7414 (mt-10)
REVERT: A  702 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7808 (ttm110)
REVERT: A  765 MET cc_start: 0.7982 (mmm) cc_final: 0.7079 (mmm)
REVERT: A  806 GLN cc_start: 0.7956 (tp40) cc_final: 0.7666 (tp40)
REVERT: A  862 LYS cc_start: 0.8361 (tppt) cc_final: 0.7936 (tppt)
REVERT: A  894 PHE cc_start: 0.8652 (t80) cc_final: 0.8225 (t80)
REVERT: B   34 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7704 (mtpt)
REVERT: B  105 LEU cc_start: 0.8462 (mp) cc_final: 0.8210 (mm)
REVERT: B  168 VAL cc_start: 0.8572 (t) cc_final: 0.8110 (m)
  outliers start: 10
  outliers final: 10
  residues processed: 134
  average time/residue: 0.2377
  time to fit residues: 37.6662
Evaluate side-chains
  138 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  773 LEU
Chi-restraints excluded: chain A residue  794 VAL
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  134 ILE
Chi-restraints excluded: chain B residue  171 LEU
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:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   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 666 ASN
A 673 GLN
B   4 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.125845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.109759 restraints weight = 6663.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.19
r_work: 0.3300 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4585  Z= 0.319
  Angle     :  0.587   7.564   6201  Z= 0.309
  Chirality :  0.044   0.155    700
  Planarity :  0.004   0.036    790
  Dihedral  :  4.615  22.227    598
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.84 %
    Favored  : 78.96 %
  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:  1.64 (0.36), residues: 552
  helix:  1.82 (0.30), residues: 298
  sheet:  0.71 (0.65), residues: 69
  loop :  0.13 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A   6 
 HIS   0.009   0.001   HIS A  33 
 PHE   0.013   0.002   PHE A 779 
 TYR   0.015   0.001   TYR A 808 
 ARG   0.006   0.001   ARG A 695 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3006.07 seconds
wall clock time: 54 minutes 21.94 seconds (3261.94 seconds total)