Starting phenix.real_space_refine
on Fri Oct 10 12:01:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sym_40884/10_2025/8sym_40884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sym_40884/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sym_40884/10_2025/8sym_40884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sym_40884/10_2025/8sym_40884.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sym_40884/10_2025/8sym_40884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sym_40884/10_2025/8sym_40884.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.18, per 1000 atoms: 0.26
  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: 0.22
  Conformation dependent library (CDL) restraints added in 109.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.15
  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: 0.66

  Time building geometry restraints manager: 0.30 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:             2.050
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.580
  Find NCS groups from input model:        0.010
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.740
-------------------------------------------------------------------------------
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 : 8.24
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (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
 ARG   0.002   0.000   ARG A 686 
 TYR   0.011   0.002   TYR A 725 
 PHE   0.013   0.002   PHE A 744 
 TRP   0.009   0.001   TRP A   6 
 HIS   0.007   0.001   HIS A  33 

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

*********************** 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  : 0.173 
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: 0.0880
  time to fit residues: 15.6998
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  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0060
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.2980
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.3996

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.127254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.110555 restraints weight = 6643.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.24
r_work: 0.3320 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1044

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= 0.169
  Angle     :  0.530   7.007   6201  Z= 0.281
  Chirality :  0.043   0.182    700
  Planarity :  0.004   0.042    790
  Dihedral  :  4.511  17.407    598
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.35), residues: 552
  helix:  1.92 (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
 ARG   0.003   0.000   ARG A 680 
 TYR   0.009   0.001   TYR A 707 
 PHE   0.014   0.002   PHE A 779 
 TRP   0.006   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 4585)
  covalent geometry    : angle       0.52987 ( 6201)
  hydrogen bonds       : bond        0.04325 (  264)
  hydrogen bonds       : angle       4.66056 (  768)

*********************** 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  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7511 (mtp180)
REVERT: A   16 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7353 (mt-10)
REVERT: A  598 GLN cc_start: 0.8078 (mp-120) cc_final: 0.7855 (mm-40)
REVERT: A  602 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8391 (mtpp)
REVERT: A  679 ASN cc_start: 0.7708 (m-40) cc_final: 0.7477 (m110)
REVERT: A  684 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7528 (mt-10)
REVERT: A  696 LYS cc_start: 0.8423 (mttt) cc_final: 0.8158 (mttt)
REVERT: A  702 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7865 (ttm110)
REVERT: A  825 LEU cc_start: 0.8950 (mt) cc_final: 0.8625 (mp)
REVERT: A  855 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7167 (mtpt)
REVERT: A  862 LYS cc_start: 0.8371 (tppt) cc_final: 0.7897 (tppt)
REVERT: A  881 ASP cc_start: 0.7793 (m-30) cc_final: 0.7424 (m-30)
REVERT: A  894 PHE cc_start: 0.8702 (t80) cc_final: 0.8291 (t80)
REVERT: B   34 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7859 (mtpt)
REVERT: B  105 LEU cc_start: 0.8427 (mp) cc_final: 0.8189 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0942
  time to fit residues: 15.3455
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  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    0.2980
   chunk 27 optimal weight:    0.0870
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.4358

-------------------------------------------------------------------------------
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 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.126970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.110358 restraints weight = 6631.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.22
r_work: 0.3320 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1341

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= 0.176
  Angle     :  0.534   6.634   6201  Z= 0.286
  Chirality :  0.043   0.187    700
  Planarity :  0.004   0.042    790
  Dihedral  :  4.516  17.168    598
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 15.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.35), residues: 552
  helix:  1.83 (0.30), residues: 297
  sheet:  0.76 (0.67), residues: 61
  loop :  0.24 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 661 
 TYR   0.009   0.001   TYR A 808 
 PHE   0.016   0.001   PHE A 779 
 TRP   0.008   0.001   TRP A   6 
 HIS   0.006   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 4585)
  covalent geometry    : angle       0.53433 ( 6201)
  hydrogen bonds       : bond        0.04168 (  264)
  hydrogen bonds       : angle       4.56259 (  768)

*********************** 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
  139 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 137
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7328 (mt-10)
REVERT: A  598 GLN cc_start: 0.8034 (mp-120) cc_final: 0.7828 (mm-40)
REVERT: A  642 LYS cc_start: 0.8010 (mtpp) cc_final: 0.7681 (ttmm)
REVERT: A  684 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7472 (mt-10)
REVERT: A  696 LYS cc_start: 0.8460 (mttt) cc_final: 0.8180 (mttt)
REVERT: A  702 ARG cc_start: 0.8095 (mtt-85) cc_final: 0.7876 (ttm110)
REVERT: A  825 LEU cc_start: 0.8947 (mt) cc_final: 0.8620 (mp)
REVERT: A  855 LYS cc_start: 0.7597 (mtpt) cc_final: 0.7260 (mtpt)
REVERT: A  862 LYS cc_start: 0.8400 (tppt) cc_final: 0.7915 (tppt)
REVERT: A  881 ASP cc_start: 0.7827 (m-30) cc_final: 0.7461 (m-30)
REVERT: A  894 PHE cc_start: 0.8704 (t80) cc_final: 0.8326 (t80)
REVERT: B   34 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7816 (mtpt)
REVERT: B  105 LEU cc_start: 0.8485 (mp) cc_final: 0.8228 (mm)
REVERT: B  168 VAL cc_start: 0.8549 (t) cc_final: 0.8072 (m)
  outliers start: 2
  outliers final: 2
  residues processed: 137
  average time/residue: 0.0978
  time to fit residues: 16.0332
Evaluate side-chains
  138 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 136
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 19 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    0.2980
   chunk 42 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0170
   chunk 10 optimal weight:    0.1980
   overall best weight:    0.3418

-------------------------------------------------------------------------------
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 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 = 0.3703 r_free = 0.3703 target = 0.127842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.111297 restraints weight = 6587.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.21
r_work: 0.3339 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1537

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= 0.149
  Angle     :  0.523   6.407   6201  Z= 0.276
  Chirality :  0.042   0.165    700
  Planarity :  0.004   0.042    790
  Dihedral  :  4.441  16.935    598
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 16.83 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.36), residues: 552
  helix:  1.94 (0.30), residues: 297
  sheet:  0.79 (0.63), residues: 71
  loop :  0.28 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 695 
 TYR   0.009   0.001   TYR A 808 
 PHE   0.013   0.001   PHE A 779 
 TRP   0.007   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4585)
  covalent geometry    : angle       0.52276 ( 6201)
  hydrogen bonds       : bond        0.03818 (  264)
  hydrogen bonds       : angle       4.46479 (  768)

*********************** 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
  141 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7393 (mt-10)
REVERT: A  642 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7721 (ttmm)
REVERT: A  651 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7141 (mt-10)
REVERT: A  679 ASN cc_start: 0.7687 (m-40) cc_final: 0.7466 (m110)
REVERT: A  684 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7431 (mt-10)
REVERT: A  696 LYS cc_start: 0.8461 (mttt) cc_final: 0.8176 (mttt)
REVERT: A  702 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7853 (ttm110)
REVERT: A  765 MET cc_start: 0.7961 (mmm) cc_final: 0.7104 (mmm)
REVERT: A  855 LYS cc_start: 0.7595 (mtpt) cc_final: 0.7254 (mtpt)
REVERT: A  862 LYS cc_start: 0.8395 (tppt) cc_final: 0.7926 (tppt)
REVERT: A  881 ASP cc_start: 0.7839 (m-30) cc_final: 0.7464 (m-30)
REVERT: A  888 SER cc_start: 0.8340 (t) cc_final: 0.8138 (p)
REVERT: A  894 PHE cc_start: 0.8699 (t80) cc_final: 0.8322 (t80)
REVERT: B  105 LEU cc_start: 0.8505 (mp) cc_final: 0.8252 (mm)
REVERT: B  168 VAL cc_start: 0.8572 (t) cc_final: 0.8092 (m)
  outliers start: 4
  outliers final: 2
  residues processed: 137
  average time/residue: 0.1027
  time to fit residues: 16.7218
Evaluate side-chains
  136 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 133
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    0.1980
   chunk 25 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0980
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.3780

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.127450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.111268 restraints weight = 6625.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.20
r_work: 0.3333 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4585  Z= 0.158
  Angle     :  0.521   6.827   6201  Z= 0.279
  Chirality :  0.042   0.143    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.400  17.491    598
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.63 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.36), residues: 552
  helix:  1.89 (0.30), residues: 297
  sheet:  0.76 (0.63), residues: 71
  loop :  0.35 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 680 
 TYR   0.010   0.001   TYR A 808 
 PHE   0.012   0.001   PHE A 779 
 TRP   0.005   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4585)
  covalent geometry    : angle       0.52113 ( 6201)
  hydrogen bonds       : bond        0.03831 (  264)
  hydrogen bonds       : angle       4.44889 (  768)

*********************** 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
  146 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8295 (mmm) cc_final: 0.7978 (mmm)
REVERT: A  642 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7796 (ttmm)
REVERT: A  651 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7113 (mt-10)
REVERT: A  679 ASN cc_start: 0.7698 (m-40) cc_final: 0.7461 (m110)
REVERT: A  684 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7433 (mt-10)
REVERT: A  696 LYS cc_start: 0.8402 (mttt) cc_final: 0.8144 (mttt)
REVERT: A  702 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7841 (ttm110)
REVERT: A  765 MET cc_start: 0.7937 (mmm) cc_final: 0.7119 (mmm)
REVERT: A  806 GLN cc_start: 0.7834 (tp40) cc_final: 0.7350 (tp-100)
REVERT: A  862 LYS cc_start: 0.8381 (tppt) cc_final: 0.7910 (tppt)
REVERT: A  881 ASP cc_start: 0.7866 (m-30) cc_final: 0.7495 (m-30)
REVERT: A  894 PHE cc_start: 0.8698 (t80) cc_final: 0.8338 (t80)
REVERT: B  105 LEU cc_start: 0.8519 (mp) cc_final: 0.8271 (mm)
REVERT: B  168 VAL cc_start: 0.8569 (t) cc_final: 0.8094 (m)
  outliers start: 7
  outliers final: 6
  residues processed: 139
  average time/residue: 0.0947
  time to fit residues: 15.7320
Evaluate side-chains
  141 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
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  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  172 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 19 optimal weight:    0.1980
   chunk 25 optimal weight:    0.5980
   chunk 10 optimal weight:    0.4980
   chunk 47 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9990
   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 598 GLN
A 666 ASN
A 833 GLN
** 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 = 0.3690 r_free = 0.3690 target = 0.127059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.110663 restraints weight = 6720.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.24
r_work: 0.3318 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4585  Z= 0.163
  Angle     :  0.523   6.731   6201  Z= 0.278
  Chirality :  0.043   0.135    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.426  18.202    598
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.03 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.36), residues: 552
  helix:  1.88 (0.30), residues: 297
  sheet:  0.74 (0.63), residues: 71
  loop :  0.37 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 695 
 TYR   0.011   0.001   TYR A 808 
 PHE   0.012   0.001   PHE A 779 
 TRP   0.005   0.001   TRP A   6 
 HIS   0.006   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4585)
  covalent geometry    : angle       0.52308 ( 6201)
  hydrogen bonds       : bond        0.03831 (  264)
  hydrogen bonds       : angle       4.42568 (  768)

*********************** 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
  137 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8295 (mmm) cc_final: 0.8094 (mmm)
REVERT: A  602 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8414 (mtpp)
REVERT: A  642 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7801 (ttmm)
REVERT: A  651 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7164 (mt-10)
REVERT: A  679 ASN cc_start: 0.7720 (m-40) cc_final: 0.7476 (m110)
REVERT: A  684 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7436 (mt-10)
REVERT: A  696 LYS cc_start: 0.8439 (mttt) cc_final: 0.8175 (mttt)
REVERT: A  702 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7839 (ttm110)
REVERT: A  765 MET cc_start: 0.7927 (mmm) cc_final: 0.7153 (mmm)
REVERT: A  804 VAL cc_start: 0.8550 (t) cc_final: 0.8309 (p)
REVERT: A  806 GLN cc_start: 0.7912 (tp40) cc_final: 0.7504 (tp-100)
REVERT: A  862 LYS cc_start: 0.8361 (tppt) cc_final: 0.7916 (tppt)
REVERT: A  894 PHE cc_start: 0.8696 (t80) cc_final: 0.8323 (t80)
REVERT: B  105 LEU cc_start: 0.8504 (mp) cc_final: 0.8258 (mm)
REVERT: B  168 VAL cc_start: 0.8585 (t) cc_final: 0.8104 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 130
  average time/residue: 0.1091
  time to fit residues: 16.7797
Evaluate side-chains
  131 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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  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  172 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0070
   chunk 16 optimal weight:    0.0570
   chunk 39 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 12 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.3316

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.127397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.111095 restraints weight = 6696.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.23
r_work: 0.3334 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4585  Z= 0.148
  Angle     :  0.520   7.003   6201  Z= 0.275
  Chirality :  0.042   0.136    700
  Planarity :  0.004   0.041    790
  Dihedral  :  4.386  18.374    598
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.23 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.36), residues: 552
  helix:  1.91 (0.30), residues: 297
  sheet:  0.76 (0.63), residues: 71
  loop :  0.37 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 695 
 TYR   0.010   0.001   TYR A 808 
 PHE   0.010   0.001   PHE A 779 
 TRP   0.004   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4585)
  covalent geometry    : angle       0.51974 ( 6201)
  hydrogen bonds       : bond        0.03720 (  264)
  hydrogen bonds       : angle       4.40841 (  768)

*********************** 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
  135 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8322 (mmm) cc_final: 0.8102 (mmm)
REVERT: A  651 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7152 (mt-10)
REVERT: A  679 ASN cc_start: 0.7678 (m-40) cc_final: 0.7445 (m110)
REVERT: A  684 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7438 (mt-10)
REVERT: A  696 LYS cc_start: 0.8392 (mttt) cc_final: 0.8143 (mttt)
REVERT: A  702 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7808 (ttm110)
REVERT: A  765 MET cc_start: 0.7911 (mmm) cc_final: 0.7175 (mmm)
REVERT: A  862 LYS cc_start: 0.8352 (tppt) cc_final: 0.7930 (tppt)
REVERT: A  894 PHE cc_start: 0.8674 (t80) cc_final: 0.8283 (t80)
REVERT: B  105 LEU cc_start: 0.8523 (mp) cc_final: 0.8286 (mm)
REVERT: B  168 VAL cc_start: 0.8587 (t) cc_final: 0.8106 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 130
  average time/residue: 0.1092
  time to fit residues: 16.8456
Evaluate side-chains
  130 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
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  805 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0030
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 29 optimal weight:    0.1980
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.4190

-------------------------------------------------------------------------------
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 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 = 0.3693 r_free = 0.3693 target = 0.127100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.110864 restraints weight = 6715.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.23
r_work: 0.3332 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1922

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= 0.173
  Angle     :  0.551   8.127   6201  Z= 0.287
  Chirality :  0.043   0.136    700
  Planarity :  0.004   0.037    790
  Dihedral  :  4.444  19.244    598
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.64 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.36), residues: 552
  helix:  1.90 (0.30), residues: 297
  sheet:  0.91 (0.64), residues: 69
  loop :  0.27 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 680 
 TYR   0.023   0.001   TYR A 725 
 PHE   0.012   0.001   PHE A 779 
 TRP   0.007   0.001   TRP A   6 
 HIS   0.006   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 4585)
  covalent geometry    : angle       0.55121 ( 6201)
  hydrogen bonds       : bond        0.03861 (  264)
  hydrogen bonds       : angle       4.42602 (  768)

*********************** 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
  133 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8308 (mmm) cc_final: 0.8053 (mmm)
REVERT: A  651 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7137 (mt-10)
REVERT: A  679 ASN cc_start: 0.7709 (m-40) cc_final: 0.7475 (m110)
REVERT: A  684 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7428 (mt-10)
REVERT: A  702 ARG cc_start: 0.7993 (mtt-85) cc_final: 0.7787 (ttm110)
REVERT: A  765 MET cc_start: 0.7914 (mmm) cc_final: 0.7204 (mmm)
REVERT: A  806 GLN cc_start: 0.7943 (tp40) cc_final: 0.7669 (tp40)
REVERT: A  862 LYS cc_start: 0.8353 (tppt) cc_final: 0.7920 (tppt)
REVERT: A  894 PHE cc_start: 0.8690 (t80) cc_final: 0.8330 (t80)
REVERT: B   34 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7695 (mtpt)
REVERT: B  105 LEU cc_start: 0.8492 (mp) cc_final: 0.8251 (mm)
REVERT: B  168 VAL cc_start: 0.8602 (t) cc_final: 0.8125 (m)
  outliers start: 9
  outliers final: 8
  residues processed: 129
  average time/residue: 0.1175
  time to fit residues: 17.8998
Evaluate side-chains
  132 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    0.2980
   chunk 7 optimal weight:    0.0010
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   chunk 9 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.3364

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.127464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.111342 restraints weight = 6698.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.24
r_work: 0.3327 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4585  Z= 0.150
  Angle     :  0.542   7.620   6201  Z= 0.284
  Chirality :  0.042   0.139    700
  Planarity :  0.004   0.038    790
  Dihedral  :  4.384  19.656    598
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 18.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.36), residues: 552
  helix:  1.97 (0.30), residues: 297
  sheet:  0.99 (0.64), residues: 69
  loop :  0.25 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 695 
 TYR   0.021   0.001   TYR A 725 
 PHE   0.010   0.001   PHE B 154 
 TRP   0.006   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4585)
  covalent geometry    : angle       0.54227 ( 6201)
  hydrogen bonds       : bond        0.03665 (  264)
  hydrogen bonds       : angle       4.39938 (  768)

*********************** 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: 8
    poor density    : 128
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8290 (mmm) cc_final: 0.8001 (mmm)
REVERT: A  651 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7221 (mt-10)
REVERT: A  679 ASN cc_start: 0.7765 (m-40) cc_final: 0.7542 (m110)
REVERT: A  684 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7371 (mt-10)
REVERT: A  702 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7825 (ttm110)
REVERT: A  765 MET cc_start: 0.7947 (mmm) cc_final: 0.7148 (mmm)
REVERT: A  806 GLN cc_start: 0.7927 (tp40) cc_final: 0.7674 (tp40)
REVERT: A  862 LYS cc_start: 0.8319 (tppt) cc_final: 0.7909 (tppt)
REVERT: A  894 PHE cc_start: 0.8669 (t80) cc_final: 0.8262 (t80)
REVERT: B  105 LEU cc_start: 0.8483 (mp) cc_final: 0.8242 (mm)
REVERT: B  168 VAL cc_start: 0.8575 (t) cc_final: 0.8104 (m)
  outliers start: 8
  outliers final: 7
  residues processed: 132
  average time/residue: 0.1063
  time to fit residues: 16.6572
Evaluate side-chains
  133 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
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  805 ILE
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 6 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 15 optimal weight:    0.2980
   chunk 10 optimal weight:    0.0980
   chunk 22 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.3380

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.127487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.111231 restraints weight = 6700.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.24
r_work: 0.3330 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4585  Z= 0.151
  Angle     :  0.545   7.498   6201  Z= 0.286
  Chirality :  0.042   0.140    700
  Planarity :  0.004   0.036    790
  Dihedral  :  4.382  20.544    598
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 19.04 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.36), residues: 552
  helix:  2.00 (0.30), residues: 297
  sheet:  1.04 (0.64), residues: 69
  loop :  0.25 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 695 
 TYR   0.020   0.001   TYR A 725 
 PHE   0.012   0.001   PHE B 154 
 TRP   0.007   0.001   TRP A   6 
 HIS   0.005   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 4585)
  covalent geometry    : angle       0.54467 ( 6201)
  hydrogen bonds       : bond        0.03673 (  264)
  hydrogen bonds       : angle       4.37174 (  768)

********************** 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
  132 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 MET cc_start: 0.8287 (mmm) cc_final: 0.8008 (mmm)
REVERT: A  651 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7247 (mt-10)
REVERT: A  679 ASN cc_start: 0.7771 (m-40) cc_final: 0.7553 (m110)
REVERT: A  684 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7385 (mt-10)
REVERT: A  702 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7814 (ttm110)
REVERT: A  765 MET cc_start: 0.7978 (mmm) cc_final: 0.7147 (mmm)
REVERT: A  806 GLN cc_start: 0.7938 (tp40) cc_final: 0.7690 (tp40)
REVERT: A  862 LYS cc_start: 0.8318 (tppt) cc_final: 0.7896 (tppt)
REVERT: A  894 PHE cc_start: 0.8667 (t80) cc_final: 0.8299 (t80)
REVERT: B  105 LEU cc_start: 0.8461 (mp) cc_final: 0.8219 (mm)
REVERT: B  168 VAL cc_start: 0.8584 (t) cc_final: 0.8110 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 128
  average time/residue: 0.1096
  time to fit residues: 16.6511
Evaluate side-chains
  130 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  805 ILE
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 35 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0870
   chunk 49 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0470
   overall best weight:    0.3656

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.127369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.111159 restraints weight = 6718.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.24
r_work: 0.3323 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4585  Z= 0.157
  Angle     :  0.544   7.605   6201  Z= 0.286
  Chirality :  0.042   0.146    700
  Planarity :  0.004   0.036    790
  Dihedral  :  4.393  21.189    598
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 19.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.36), residues: 552
  helix:  2.01 (0.30), residues: 297
  sheet:  1.01 (0.64), residues: 69
  loop :  0.25 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 695 
 TYR   0.021   0.001   TYR A 725 
 PHE   0.012   0.001   PHE B 154 
 TRP   0.007   0.001   TRP A   6 
 HIS   0.006   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 4585)
  covalent geometry    : angle       0.54352 ( 6201)
  hydrogen bonds       : bond        0.03710 (  264)
  hydrogen bonds       : angle       4.36523 (  768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1348.68 seconds
wall clock time: 23 minutes 51.58 seconds (1431.58 seconds total)