Starting phenix.real_space_refine
on Sat Apr  4 21:34:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wqw_32714/04_2026/7wqw_32714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wqw_32714/04_2026/7wqw_32714.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/7wqw_32714/04_2026/7wqw_32714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wqw_32714/04_2026/7wqw_32714.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wqw_32714/04_2026/7wqw_32714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wqw_32714/04_2026/7wqw_32714.cif"
  }
  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=  -0.001 sd=   0.020
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      29      5.16       5
     C    2501      2.51       5
     N     678      2.21       5
     O     775      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3983
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2013
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2013
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 15, 'TRANS': 245}
    Chain: "B"
      Number of atoms: 1844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1844
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 220}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.14, per 1000 atoms: 0.29
  Number of scatterers: 3983
  At special positions: 0
  Unit cell: (64.852, 86.818, 96.232, 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      29     16.00
     O     775      8.00
     N     678      7.00
     C    2501      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 650 " - pdb=" SG  CYS A 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 716 " - pdb=" SG  CYS A 767 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 772 " - pdb=" SG  CYS B 896 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 810 " - pdb=" SG  CYS B 826 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 910 " - pdb=" SG  CYS B 977 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 941 " - pdb=" SG  CYS B 956 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 967 " - pdb=" SG  CYS B 995 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 801 " - " ASN A 725 "
      " NAG A 802 " - " ASN A 706 "
      " NAG A 803 " - " ASN A 682 "
      " NAG A 804 " - " ASN A 630 "
      " NAG A 805 " - " ASN A 534 "
      " NAG B1101 " - " ASN B 949 "
      " NAG B1102 " - " ASN B 909 "
      " NAG B1103 " - " ASN B 887 "
      " NAG B1104 " - " ASN B 848 "
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 149.2 milliseconds
  

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  904

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 7 sheets defined
      7.9% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 671 through 675
      removed outlier: 3.550A  pdb=" N   GLU A 674 " --> pdb=" O   GLY A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 719
    Processing helix  chain 'B' and resid 833 through 835
      No H-bonds generated for 'chain 'B' and resid 833 through 835'
    Processing helix  chain 'B' and resid 937 through 945
    Processing helix  chain 'B' and resid 1010 through 1019
      removed outlier: 4.079A  pdb=" N   PHE B1017 " --> pdb=" O   TRP B1013 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   HIS B1019 " --> pdb=" O   GLN B1015 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 538
      removed outlier: 3.565A  pdb=" N   ALA A 629 " --> pdb=" O   PHE A 537 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   ASN A 630 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
      removed outlier: 5.445A  pdb=" N   PHE A 568 " --> pdb=" O   ASN A 630 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 557
      removed outlier: 3.569A  pdb=" N   CYS A 552 " --> pdb=" O   LEU A 616 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A 616 " --> pdb=" O   CYS A 552 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   VAL A 614 " --> pdb=" O   TRP A 554 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 688 through 689
    Processing sheet with id=AA4, first strand: chain 'A' and resid 693 through 694
    Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 703
      removed outlier: 4.693A  pdb=" N   LEU A 741 " --> pdb=" O   CYS A 703 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS A 740 " --> pdb=" O   THR A 752 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR A 752 " --> pdb=" O   LYS A 740 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A 750 " --> pdb=" O   ASN A 742 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 789 through 790
      removed outlier: 3.586A  pdb=" N   GLN B 929 " --> pdb=" O   GLY B 914 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ASN B 909 " --> pdb=" O   GLN B 978 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   GLN B 978 " --> pdb=" O   ASN B 909 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ALA B 913 " --> pdb=" O   PRO B 974 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY B 987 " --> pdb=" O   LEU B 975 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   CYS B 977 " --> pdb=" O   LEU B 985 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   LEU B 985 " --> pdb=" O   CYS B 977 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   VAL B1003 " --> pdb=" O   SER B 990 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 799 through 804
      removed outlier: 3.612A  pdb=" N   CYS B 810 " --> pdb=" O   LEU B 802 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TYR B 804 " --> pdb=" O   LEU B 808 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   LEU B 808 " --> pdb=" O   TYR B 804 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLU B 861 " --> pdb=" O   HIS B 881 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   TRP B 837 " --> pdb=" O   ILE B 859 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    210 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: 0.67

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1312
        1.34 -     1.46: 901
        1.46 -     1.58: 1831
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 4080
  Sorted by residual:
  bond pdb=" C1  NAG A 804 "
       pdb=" O5  NAG A 804 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.48e+00
  bond pdb=" C1  NAG A 802 "
       pdb=" O5  NAG A 802 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.30e+00
  bond pdb=" C1  NAG A 805 "
       pdb=" O5  NAG A 805 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.16e+00
  bond pdb=" C1  NAG A 801 "
       pdb=" O5  NAG A 801 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.08e+00
  bond pdb=" C1  NAG B1104 "
       pdb=" O5  NAG B1104 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.03e+00
  ... (remaining 4075 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 5220
        0.91 -     1.82: 248
        1.82 -     2.74: 72
        2.74 -     3.65: 11
        3.65 -     4.56: 3
  Bond angle restraints: 5554
  Sorted by residual:
  angle pdb=" N   GLY A 585 "
        pdb=" CA  GLY A 585 "
        pdb=" C   GLY A 585 "
      ideal   model   delta    sigma   weight residual
     113.18  117.25   -4.07 2.37e+00 1.78e-01 2.96e+00
  angle pdb=" C   ASN A 575 "
        pdb=" N   ILE A 576 "
        pdb=" CA  ILE A 576 "
      ideal   model   delta    sigma   weight residual
     120.62  123.15   -2.53 1.64e+00 3.72e-01 2.38e+00
  angle pdb=" C   ASN A 682 "
        pdb=" N   GLY A 683 "
        pdb=" CA  GLY A 683 "
      ideal   model   delta    sigma   weight residual
     122.80  121.37    1.43 9.70e-01 1.06e+00 2.19e+00
  angle pdb=" CA  GLN A 759 "
        pdb=" CB  GLN A 759 "
        pdb=" CG  GLN A 759 "
      ideal   model   delta    sigma   weight residual
     114.10  117.04   -2.94 2.00e+00 2.50e-01 2.16e+00
  angle pdb=" NE  ARG B 830 "
        pdb=" CZ  ARG B 830 "
        pdb=" NH1 ARG B 830 "
      ideal   model   delta    sigma   weight residual
     121.50  120.05    1.45 1.00e+00 1.00e+00 2.11e+00
  ... (remaining 5549 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.35: 2391
       16.35 -    32.69: 113
       32.69 -    49.04: 28
       49.04 -    65.38: 10
       65.38 -    81.73: 2
  Dihedral angle restraints: 2544
    sinusoidal: 1132
      harmonic: 1412
  Sorted by residual:
  dihedral pdb=" CA  SER A 539 "
           pdb=" C   SER A 539 "
           pdb=" N   THR A 540 "
           pdb=" CA  THR A 540 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.41   17.59     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" N   ASN B 848 "
           pdb=" CA  ASN B 848 "
           pdb=" CB  ASN B 848 "
           pdb=" CG  ASN B 848 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.53  -58.47     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" N   CYS A 662 "
           pdb=" CA  CYS A 662 "
           pdb=" CB  CYS A 662 "
           pdb=" SG  CYS A 662 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.30   57.30     3      1.50e+01 4.44e-03 9.43e+00
  ... (remaining 2541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 416
       0.035 -    0.069: 132
       0.069 -    0.104: 55
       0.104 -    0.138: 24
       0.138 -    0.173: 1
  Chirality restraints: 628
  Sorted by residual:
  chirality pdb=" C1  NAG A 804 "
            pdb=" ND2 ASN A 630 "
            pdb=" C2  NAG A 804 "
            pdb=" O5  NAG A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CA  VAL B 919 "
            pdb=" N   VAL B 919 "
            pdb=" C   VAL B 919 "
            pdb=" CB  VAL B 919 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.95e-01
  chirality pdb=" CA  ILE B 862 "
            pdb=" N   ILE B 862 "
            pdb=" C   ILE B 862 "
            pdb=" CB  ILE B 862 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.58e-01
  ... (remaining 625 not shown)

  Planarity restraints: 731
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 542 "   -0.020 5.00e-02 4.00e+02   2.93e-02 1.38e+00
        pdb=" N   PRO A 543 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 543 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 543 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 526 "    0.017 5.00e-02 4.00e+02   2.51e-02 1.01e+00
        pdb=" N   PRO A 527 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 527 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 527 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 532 "   -0.016 5.00e-02 4.00e+02   2.44e-02 9.54e-01
        pdb=" N   PRO A 533 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 533 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 533 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 728 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1028
        2.80 -     3.32: 3674
        3.32 -     3.85: 6640
        3.85 -     4.37: 7574
        4.37 -     4.90: 12826
  Nonbonded interactions: 31742
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 584 "
            pdb=" OG1 THR A 609 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD1 ASP B 874 "
            pdb=" OG1 THR B 951 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OD2 ASP A 584 "
            pdb=" OG1 THR A 608 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OD2 ASP B 874 "
            pdb=" ND2 ASN B 875 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" NZ  LYS A 740 "
            pdb=" O   SER A 754 "
     model   vdw
     2.359 3.120
  ... (remaining 31737 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:             1.630
  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:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.650
  Find NCS groups from input model:        0.020
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
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      :  0.003   0.031   4097  Z= 0.145
  Angle     :  0.493   4.561   5597  Z= 0.249
  Chirality :  0.043   0.173    628
  Planarity :  0.003   0.029    722
  Dihedral  : 10.247  81.731   1616
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  :  6.59 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -4.30 (0.31), residues: 492
  helix: -2.87 (0.53), residues: 36
  sheet: -2.55 (0.41), residues: 127
  loop : -3.18 (0.29), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 624 
 TYR   0.003   0.000   TYR B 828 
 PHE   0.004   0.001   PHE A 537 
 TRP   0.002   0.000   TRP B 796 
 HIS   0.001   0.000   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4080)
  covalent geometry    : angle       0.48785 ( 5554)
  SS BOND              : bond        0.00138 (    8)
  SS BOND              : angle       0.52167 (   16)
  hydrogen bonds       : bond        0.25806 (   82)
  hydrogen bonds       : angle      10.55908 (  210)
  link_NAG-ASN         : bond        0.00333 (    9)
  link_NAG-ASN         : angle       1.13550 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 THR cc_start: 0.6611 (p) cc_final: 0.6249 (p)
REVERT: A  648 PHE cc_start: 0.8536 (t80) cc_final: 0.8301 (t80)
REVERT: A  700 HIS cc_start: 0.5600 (OUTLIER) cc_final: 0.4600 (p90)
REVERT: B  848 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6971 (m-40)
REVERT: B  968 GLN cc_start: 0.7087 (pm20) cc_final: 0.6773 (pt0)
  outliers start: 19
  outliers final: 5
  residues processed: 133
  average time/residue: 0.0948
  time to fit residues: 14.8742
Evaluate side-chains
  71 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  700 HIS
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 636 HIS
A 713 ASN
A 717 GLN
B 881 HIS
B 921 GLN
B 944 GLN
B 968 GLN
B 978 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.134055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.097470 restraints weight = 6535.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 3.21
r_work: 0.3280 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4097  Z= 0.214
  Angle     :  0.662   5.838   5597  Z= 0.340
  Chirality :  0.048   0.190    628
  Planarity :  0.005   0.040    722
  Dihedral  :  7.696  58.812    728
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 15.06 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -3.66 (0.35), residues: 492
  helix: -2.03 (0.70), residues: 38
  sheet: -2.54 (0.38), residues: 149
  loop : -2.51 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 940 
 TYR   0.014   0.002   TYR B 868 
 PHE   0.014   0.002   PHE B 884 
 TRP   0.008   0.002   TRP B 983 
 HIS   0.020   0.003   HIS A 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 4080)
  covalent geometry    : angle       0.64844 ( 5554)
  SS BOND              : bond        0.00681 (    8)
  SS BOND              : angle       1.78733 (   16)
  hydrogen bonds       : bond        0.04134 (   82)
  hydrogen bonds       : angle       6.80571 (  210)
  link_NAG-ASN         : bond        0.00349 (    9)
  link_NAG-ASN         : angle       1.57688 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  573 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7972 (mt)
REVERT: A  693 PHE cc_start: 0.8787 (m-80) cc_final: 0.8346 (m-80)
REVERT: A  700 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.4349 (p90)
REVERT: B  848 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7183 (m-40)
REVERT: B  873 LYS cc_start: 0.8431 (mttt) cc_final: 0.8190 (mttt)
REVERT: B  959 TYR cc_start: 0.7828 (m-80) cc_final: 0.7520 (m-80)
  outliers start: 21
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0790
  time to fit residues: 7.6192
Evaluate side-chains
  65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  700 HIS
Chi-restraints excluded: chain A residue  717 GLN
Chi-restraints excluded: chain A residue  738 PHE
Chi-restraints excluded: chain A residue  739 VAL
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  884 PHE
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.133599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.097374 restraints weight = 6381.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 3.11
r_work: 0.3281 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4097  Z= 0.141
  Angle     :  0.587   5.818   5597  Z= 0.298
  Chirality :  0.046   0.228    628
  Planarity :  0.004   0.044    722
  Dihedral  :  6.727  58.228    723
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 14.12 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -3.40 (0.35), residues: 492
  helix: -1.85 (0.74), residues: 38
  sheet: -2.34 (0.38), residues: 153
  loop : -2.32 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 692 
 TYR   0.011   0.001   TYR B 993 
 PHE   0.013   0.001   PHE A 606 
 TRP   0.007   0.001   TRP B 983 
 HIS   0.006   0.001   HIS A 769 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4080)
  covalent geometry    : angle       0.56991 ( 5554)
  SS BOND              : bond        0.00469 (    8)
  SS BOND              : angle       1.66467 (   16)
  hydrogen bonds       : bond        0.03378 (   82)
  hydrogen bonds       : angle       6.29902 (  210)
  link_NAG-ASN         : bond        0.00463 (    9)
  link_NAG-ASN         : angle       1.74281 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  636 HIS cc_start: 0.6411 (p90) cc_final: 0.6173 (p-80)
REVERT: A  639 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8450 (pt)
REVERT: A  679 ARG cc_start: 0.7757 (ptt90) cc_final: 0.7407 (ptt90)
REVERT: A  693 PHE cc_start: 0.8815 (m-80) cc_final: 0.8388 (m-80)
REVERT: A  700 HIS cc_start: 0.5736 (OUTLIER) cc_final: 0.4909 (p90)
REVERT: A  750 ILE cc_start: 0.8478 (mp) cc_final: 0.8146 (tt)
REVERT: A  772 CYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7038 (t)
REVERT: B  848 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7215 (m-40)
  outliers start: 22
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0675
  time to fit residues: 6.2317
Evaluate side-chains
  74 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  700 HIS
Chi-restraints excluded: chain A residue  738 PHE
Chi-restraints excluded: chain A residue  739 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  884 PHE
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  951 THR
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 20 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.132182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.095686 restraints weight = 6405.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 3.17
r_work: 0.3259 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.4217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4097  Z= 0.145
  Angle     :  0.568   5.621   5597  Z= 0.288
  Chirality :  0.046   0.217    628
  Planarity :  0.004   0.043    722
  Dihedral  :  6.523  58.139    723
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 15.06 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.36), residues: 492
  helix: -1.46 (0.76), residues: 38
  sheet: -2.37 (0.37), residues: 161
  loop : -1.87 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 692 
 TYR   0.006   0.001   TYR B 920 
 PHE   0.019   0.001   PHE A 681 
 TRP   0.006   0.001   TRP B 983 
 HIS   0.004   0.001   HIS A 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4080)
  covalent geometry    : angle       0.55013 ( 5554)
  SS BOND              : bond        0.00391 (    8)
  SS BOND              : angle       1.56062 (   16)
  hydrogen bonds       : bond        0.03144 (   82)
  hydrogen bonds       : angle       5.97257 (  210)
  link_NAG-ASN         : bond        0.00452 (    9)
  link_NAG-ASN         : angle       1.81423 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  636 HIS cc_start: 0.6605 (p90) cc_final: 0.6353 (p-80)
REVERT: A  639 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8439 (pt)
REVERT: A  693 PHE cc_start: 0.8823 (m-80) cc_final: 0.8548 (m-80)
REVERT: A  750 ILE cc_start: 0.8528 (mp) cc_final: 0.8183 (tt)
REVERT: A  772 CYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6985 (t)
REVERT: B  845 MET cc_start: 0.8510 (mtm) cc_final: 0.8259 (mtp)
REVERT: B  848 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7293 (m-40)
  outliers start: 16
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0700
  time to fit residues: 5.8319
Evaluate side-chains
  58 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  739 VAL
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 45 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 548 ASN
A 647 HIS
** B 844 HIS ** 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 = 0.3926 r_free = 0.3926 target = 0.131829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.095461 restraints weight = 6373.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 3.14
r_work: 0.3254 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.4547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4097  Z= 0.155
  Angle     :  0.595   6.362   5597  Z= 0.304
  Chirality :  0.046   0.215    628
  Planarity :  0.004   0.043    722
  Dihedral  :  6.525  57.942    721
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.24 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.94 (0.36), residues: 492
  helix: -1.34 (0.78), residues: 38
  sheet: -2.22 (0.38), residues: 150
  loop : -1.91 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 624 
 TYR   0.006   0.001   TYR B1004 
 PHE   0.011   0.001   PHE A 537 
 TRP   0.006   0.001   TRP B 983 
 HIS   0.005   0.001   HIS A 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4080)
  covalent geometry    : angle       0.57711 ( 5554)
  SS BOND              : bond        0.00397 (    8)
  SS BOND              : angle       1.61551 (   16)
  hydrogen bonds       : bond        0.03114 (   82)
  hydrogen bonds       : angle       5.96559 (  210)
  link_NAG-ASN         : bond        0.00463 (    9)
  link_NAG-ASN         : angle       1.83896 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  636 HIS cc_start: 0.6530 (p90) cc_final: 0.6288 (p-80)
REVERT: A  639 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8479 (pt)
REVERT: A  647 HIS cc_start: 0.6274 (m170) cc_final: 0.6011 (m-70)
REVERT: A  648 PHE cc_start: 0.8656 (t80) cc_final: 0.8326 (t80)
REVERT: A  681 PHE cc_start: 0.7542 (t80) cc_final: 0.7266 (t80)
REVERT: A  692 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7379 (tpp80)
REVERT: A  693 PHE cc_start: 0.8855 (m-80) cc_final: 0.8595 (m-10)
REVERT: A  700 HIS cc_start: 0.6127 (OUTLIER) cc_final: 0.4595 (p90)
REVERT: A  750 ILE cc_start: 0.8478 (mp) cc_final: 0.8134 (tt)
REVERT: A  772 CYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6852 (t)
REVERT: B  845 MET cc_start: 0.8552 (mtm) cc_final: 0.8309 (mtp)
REVERT: B  848 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7257 (m-40)
  outliers start: 17
  outliers final: 9
  residues processed: 68
  average time/residue: 0.0730
  time to fit residues: 6.1787
Evaluate side-chains
  63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  700 HIS
Chi-restraints excluded: chain A residue  739 VAL
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  884 PHE
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.139568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.107088 restraints weight = 6558.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.65
r_work: 0.3550 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.4743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4097  Z= 0.158
  Angle     :  0.591   5.882   5597  Z= 0.304
  Chirality :  0.046   0.213    628
  Planarity :  0.004   0.042    722
  Dihedral  :  6.597  58.143    721
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.00 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.79 (0.36), residues: 492
  helix: -1.28 (0.78), residues: 38
  sheet: -1.99 (0.44), residues: 118
  loop : -1.97 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 679 
 TYR   0.013   0.001   TYR B 959 
 PHE   0.011   0.001   PHE A 537 
 TRP   0.032   0.002   TRP A 699 
 HIS   0.005   0.001   HIS A 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4080)
  covalent geometry    : angle       0.57274 ( 5554)
  SS BOND              : bond        0.00379 (    8)
  SS BOND              : angle       1.60182 (   16)
  hydrogen bonds       : bond        0.03038 (   82)
  hydrogen bonds       : angle       5.84578 (  210)
  link_NAG-ASN         : bond        0.00472 (    9)
  link_NAG-ASN         : angle       1.84854 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  639 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8502 (pt)
REVERT: A  647 HIS cc_start: 0.6001 (m170) cc_final: 0.5777 (m-70)
REVERT: A  648 PHE cc_start: 0.8522 (t80) cc_final: 0.8289 (t80)
REVERT: A  700 HIS cc_start: 0.6282 (OUTLIER) cc_final: 0.4881 (p90)
REVERT: A  750 ILE cc_start: 0.8387 (mp) cc_final: 0.8088 (tt)
REVERT: A  772 CYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7295 (t)
REVERT: B  845 MET cc_start: 0.8570 (mtm) cc_final: 0.8300 (mtp)
REVERT: B  848 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7565 (m-40)
  outliers start: 17
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0717
  time to fit residues: 6.1480
Evaluate side-chains
  60 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  700 HIS
Chi-restraints excluded: chain A residue  739 VAL
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  884 PHE
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 36 optimal weight:    0.0870
   chunk 47 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0030
   chunk 42 optimal weight:    0.2980
   chunk 44 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0870
   chunk 3 optimal weight:    0.0980
   overall best weight:    0.1146

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

Flipped N/Q/H residues before XYZ refinement:
A 768 ASN
** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 844 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.143791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.111649 restraints weight = 6554.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 2.69
r_work: 0.3666 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3526 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4097  Z= 0.105
  Angle     :  0.568   5.959   5597  Z= 0.293
  Chirality :  0.046   0.232    628
  Planarity :  0.004   0.041    722
  Dihedral  :  6.337  57.456    721
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 17.65 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.74 (0.37), residues: 492
  helix: -0.92 (0.80), residues: 38
  sheet: -2.19 (0.38), residues: 155
  loop : -1.73 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 679 
 TYR   0.013   0.001   TYR A 546 
 PHE   0.010   0.001   PHE A 606 
 TRP   0.009   0.001   TRP A 699 
 HIS   0.002   0.001   HIS A 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 4080)
  covalent geometry    : angle       0.55150 ( 5554)
  SS BOND              : bond        0.00298 (    8)
  SS BOND              : angle       1.29468 (   16)
  hydrogen bonds       : bond        0.02707 (   82)
  hydrogen bonds       : angle       5.51259 (  210)
  link_NAG-ASN         : bond        0.00519 (    9)
  link_NAG-ASN         : angle       1.83484 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  647 HIS cc_start: 0.5973 (m170) cc_final: 0.5697 (m-70)
REVERT: A  648 PHE cc_start: 0.8527 (t80) cc_final: 0.8314 (t80)
REVERT: A  676 ASP cc_start: 0.8187 (p0) cc_final: 0.7807 (p0)
REVERT: A  700 HIS cc_start: 0.5990 (OUTLIER) cc_final: 0.4941 (p90)
REVERT: A  750 ILE cc_start: 0.8526 (mp) cc_final: 0.8131 (tt)
REVERT: A  772 CYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7378 (t)
REVERT: B  848 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7489 (m-40)
  outliers start: 16
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0633
  time to fit residues: 5.7255
Evaluate side-chains
  64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain A residue  700 HIS
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  884 PHE
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    0.1980
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 779 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.140033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.107621 restraints weight = 6462.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.64
r_work: 0.3575 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4097  Z= 0.155
  Angle     :  0.608   6.760   5597  Z= 0.315
  Chirality :  0.047   0.212    628
  Planarity :  0.004   0.042    722
  Dihedral  :  6.547  57.598    721
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 17.65 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.57 (0.37), residues: 492
  helix: -0.95 (0.81), residues: 38
  sheet: -1.72 (0.42), residues: 137
  loop : -1.86 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 624 
 TYR   0.014   0.001   TYR B 959 
 PHE   0.010   0.001   PHE A 537 
 TRP   0.005   0.001   TRP B 796 
 HIS   0.002   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4080)
  covalent geometry    : angle       0.59170 ( 5554)
  SS BOND              : bond        0.00375 (    8)
  SS BOND              : angle       1.47877 (   16)
  hydrogen bonds       : bond        0.02890 (   82)
  hydrogen bonds       : angle       5.77326 (  210)
  link_NAG-ASN         : bond        0.00467 (    9)
  link_NAG-ASN         : angle       1.83821 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  647 HIS cc_start: 0.6005 (m170) cc_final: 0.5786 (m-70)
REVERT: A  648 PHE cc_start: 0.8548 (t80) cc_final: 0.8328 (t80)
REVERT: A  700 HIS cc_start: 0.6041 (OUTLIER) cc_final: 0.5307 (p90)
REVERT: A  750 ILE cc_start: 0.8372 (mp) cc_final: 0.8039 (tt)
REVERT: A  772 CYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7297 (t)
  outliers start: 18
  outliers final: 12
  residues processed: 69
  average time/residue: 0.0661
  time to fit residues: 5.7649
Evaluate side-chains
  65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain A residue  651 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain A residue  700 HIS
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  884 PHE
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 33 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.140584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.108141 restraints weight = 6579.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.70
r_work: 0.3601 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.4993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4097  Z= 0.142
  Angle     :  0.608   5.822   5597  Z= 0.315
  Chirality :  0.047   0.218    628
  Planarity :  0.004   0.038    722
  Dihedral  :  6.489  57.404    721
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.00 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.61 (0.36), residues: 492
  helix: -1.00 (0.81), residues: 38
  sheet: -1.74 (0.42), residues: 137
  loop : -1.89 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 982 
 TYR   0.013   0.001   TYR A 546 
 PHE   0.012   0.001   PHE B1017 
 TRP   0.005   0.001   TRP B 983 
 HIS   0.002   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4080)
  covalent geometry    : angle       0.59192 ( 5554)
  SS BOND              : bond        0.00368 (    8)
  SS BOND              : angle       1.49255 (   16)
  hydrogen bonds       : bond        0.02872 (   82)
  hydrogen bonds       : angle       5.81516 (  210)
  link_NAG-ASN         : bond        0.00479 (    9)
  link_NAG-ASN         : angle       1.82443 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  647 HIS cc_start: 0.5901 (m170) cc_final: 0.5661 (m-70)
REVERT: A  750 ILE cc_start: 0.8374 (mp) cc_final: 0.8070 (tt)
REVERT: A  772 CYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7293 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 61
  average time/residue: 0.0672
  time to fit residues: 5.2178
Evaluate side-chains
  59 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 1 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 14 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.139076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.106858 restraints weight = 6511.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.63
r_work: 0.3564 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3420 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4097  Z= 0.167
  Angle     :  0.627   5.562   5597  Z= 0.325
  Chirality :  0.047   0.212    628
  Planarity :  0.004   0.042    722
  Dihedral  :  6.681  58.000    721
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.37 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.29 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.62 (0.36), residues: 492
  helix: -1.01 (0.82), residues: 38
  sheet: -1.70 (0.45), residues: 114
  loop : -1.95 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 679 
 TYR   0.007   0.001   TYR B 828 
 PHE   0.013   0.001   PHE B1017 
 TRP   0.010   0.001   TRP A 699 
 HIS   0.002   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4080)
  covalent geometry    : angle       0.61020 ( 5554)
  SS BOND              : bond        0.00389 (    8)
  SS BOND              : angle       1.57376 (   16)
  hydrogen bonds       : bond        0.02936 (   82)
  hydrogen bonds       : angle       5.85649 (  210)
  link_NAG-ASN         : bond        0.00467 (    9)
  link_NAG-ASN         : angle       1.85758 (   27)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  647 HIS cc_start: 0.5968 (m170) cc_final: 0.5716 (m-70)
REVERT: A  750 ILE cc_start: 0.8371 (mp) cc_final: 0.8066 (tt)
REVERT: A  772 CYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7320 (t)
  outliers start: 9
  outliers final: 8
  residues processed: 58
  average time/residue: 0.0606
  time to fit residues: 4.5748
Evaluate side-chains
  59 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.138552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.106184 restraints weight = 6573.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.69
r_work: 0.3577 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.5281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4097  Z= 0.168
  Angle     :  0.638   6.052   5597  Z= 0.330
  Chirality :  0.047   0.214    628
  Planarity :  0.004   0.040    722
  Dihedral  :  6.727  58.240    721
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.76 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.61 (0.36), residues: 492
  helix: -1.01 (0.82), residues: 38
  sheet: -1.57 (0.44), residues: 120
  loop : -1.98 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 679 
 TYR   0.017   0.002   TYR B 959 
 PHE   0.013   0.001   PHE B1017 
 TRP   0.010   0.001   TRP A 699 
 HIS   0.002   0.001   HIS A 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 4080)
  covalent geometry    : angle       0.62151 ( 5554)
  SS BOND              : bond        0.00401 (    8)
  SS BOND              : angle       1.53986 (   16)
  hydrogen bonds       : bond        0.02969 (   82)
  hydrogen bonds       : angle       5.97086 (  210)
  link_NAG-ASN         : bond        0.00468 (    9)
  link_NAG-ASN         : angle       1.84876 (   27)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1311.17 seconds
wall clock time: 23 minutes 4.29 seconds (1384.29 seconds total)