Starting phenix.real_space_refine
on Wed Jun  4 20:33:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wqw_32714/06_2025/7wqw_32714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wqw_32714/06_2025/7wqw_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_32714/06_2025/7wqw_32714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wqw_32714/06_2025/7wqw_32714.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wqw_32714/06_2025/7wqw_32714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wqw_32714/06_2025/7wqw_32714.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.23, per 1000 atoms: 0.81
  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: 1.04
  Conformation dependent library (CDL) restraints added in 517.5 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: 0.40
  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: 0.95

  Time building geometry restraints manager: 1.24 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:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.310
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.700
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.002   0.000   TRP B 796 
 HIS   0.001   0.000   HIS A 665 
 PHE   0.004   0.001   PHE A 537 
 TYR   0.003   0.000   TYR B 828 
 ARG   0.002   0.000   ARG A 624 

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

*********************** 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  : 0.421 
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: 0.6247 (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: 0.4602 (p90)
REVERT: B  848 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6981 (m-40)
REVERT: B  968 GLN cc_start: 0.7087 (pm20) cc_final: 0.6774 (pt0)
  outliers start: 19
  outliers final: 5
  residues processed: 133
  average time/residue: 0.2029
  time to fit residues: 31.9345
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  : 0.437 
-------------------------------------------------------------------------------
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 41 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 28 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS
B 875 ASN
B 881 HIS
B 921 GLN
B 944 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.138155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.101946 restraints weight = 6367.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 3.16
r_work: 0.3358 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3112

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= 0.152
  Angle     :  0.602   5.305   5597  Z= 0.309
  Chirality :  0.047   0.183    628
  Planarity :  0.004   0.031    722
  Dihedral  :  7.436  58.404    728
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 14.59 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.71 (0.34), residues: 492
  helix: -2.03 (0.68), residues: 38
  sheet: -2.42 (0.38), residues: 148
  loop : -2.64 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 983 
 HIS   0.019   0.002   HIS A 636 
 PHE   0.010   0.001   PHE B1017 
 TYR   0.011   0.001   TYR B 993 
 ARG   0.008   0.001   ARG A 764 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00387 (    9)
  link_NAG-ASN         : angle       1.38983 (   27)
  hydrogen bonds       : bond        0.04118 (   82)
  hydrogen bonds       : angle       6.76714 (  210)
  SS BOND              : bond        0.00847 (    8)
  SS BOND              : angle       1.32340 (   16)
  covalent geometry    : bond        0.00343 ( 4080)
  covalent geometry    : angle       0.59180 ( 5554)

*********************** 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: 20
    poor density    : 65
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 THR cc_start: 0.7432 (p) cc_final: 0.7004 (p)
REVERT: A  647 HIS cc_start: 0.6387 (m170) cc_final: 0.6108 (m170)
REVERT: A  648 PHE cc_start: 0.8658 (t80) cc_final: 0.8264 (t80)
REVERT: A  693 PHE cc_start: 0.8769 (m-80) cc_final: 0.8255 (m-80)
REVERT: A  700 HIS cc_start: 0.6026 (OUTLIER) cc_final: 0.4158 (p90)
REVERT: A  750 ILE cc_start: 0.8464 (mp) cc_final: 0.8145 (tt)
REVERT: A  772 CYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6694 (t)
REVERT: B  793 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7770 (pt0)
REVERT: B  848 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7180 (m-40)
  outliers start: 20
  outliers final: 10
  residues processed: 79
  average time/residue: 0.1864
  time to fit residues: 17.8892
Evaluate side-chains
  69 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 THR
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  738 PHE
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  793 GLU
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  952 GLU
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 11 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 968 GLN
B 978 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.134491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.097963 restraints weight = 6291.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 3.13
r_work: 0.3308 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4097  Z= 0.153
  Angle     :  0.580   6.450   5597  Z= 0.295
  Chirality :  0.046   0.188    628
  Planarity :  0.004   0.034    722
  Dihedral  :  7.122  58.878    726
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 15.76 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.35), residues: 492
  helix: -1.49 (0.75), residues: 38
  sheet: -2.37 (0.37), residues: 164
  loop : -2.28 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 983 
 HIS   0.003   0.001   HIS A 636 
 PHE   0.014   0.001   PHE A 681 
 TYR   0.010   0.001   TYR B 803 
 ARG   0.003   0.001   ARG A 764 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00404 (    9)
  link_NAG-ASN         : angle       1.37665 (   27)
  hydrogen bonds       : bond        0.03429 (   82)
  hydrogen bonds       : angle       6.20546 (  210)
  SS BOND              : bond        0.00490 (    8)
  SS BOND              : angle       1.18380 (   16)
  covalent geometry    : bond        0.00353 ( 4080)
  covalent geometry    : angle       0.57060 ( 5554)

*********************** 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
  76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: A  647 HIS cc_start: 0.6479 (m170) cc_final: 0.6224 (m170)
REVERT: A  693 PHE cc_start: 0.8768 (m-80) cc_final: 0.8384 (m-80)
REVERT: A  700 HIS cc_start: 0.5724 (OUTLIER) cc_final: 0.4735 (p90)
REVERT: A  750 ILE cc_start: 0.8472 (mp) cc_final: 0.8133 (tt)
REVERT: A  772 CYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6725 (t)
REVERT: B  848 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7210 (m-40)
REVERT: B  959 TYR cc_start: 0.7701 (m-80) cc_final: 0.7437 (m-80)
REVERT: B  970 ASP cc_start: 0.7658 (t0) cc_final: 0.7454 (t0)
  outliers start: 19
  outliers final: 10
  residues processed: 72
  average time/residue: 0.1818
  time to fit residues: 16.1883
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  : 0.466 
-------------------------------------------------------------------------------
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  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  743 THR
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  896 CYS
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 28 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 548 ASN
A 687 ASN
B 844 HIS
B 875 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.126925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.090411 restraints weight = 6504.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 3.08
r_work: 0.3174 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.4903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   4097  Z= 0.289
  Angle     :  0.698   6.417   5597  Z= 0.357
  Chirality :  0.050   0.190    628
  Planarity :  0.005   0.072    722
  Dihedral  :  7.867  59.348    726
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.57 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 14.35 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.36), residues: 492
  helix: -1.55 (0.70), residues: 38
  sheet: -2.13 (0.44), residues: 120
  loop : -2.14 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 796 
 HIS   0.006   0.001   HIS A 636 
 PHE   0.019   0.002   PHE A 681 
 TYR   0.013   0.002   TYR B 868 
 ARG   0.003   0.000   ARG B 908 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00416 (    9)
  link_NAG-ASN         : angle       2.01027 (   27)
  hydrogen bonds       : bond        0.04028 (   82)
  hydrogen bonds       : angle       6.53627 (  210)
  SS BOND              : bond        0.00554 (    8)
  SS BOND              : angle       1.65297 (   16)
  covalent geometry    : bond        0.00682 ( 4080)
  covalent geometry    : angle       0.68105 ( 5554)

*********************** 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
  75 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
REVERT: A  636 HIS cc_start: 0.6779 (p90) cc_final: 0.6561 (p90)
REVERT: A  639 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8555 (pt)
REVERT: A  648 PHE cc_start: 0.8601 (t80) cc_final: 0.8242 (t80)
REVERT: A  693 PHE cc_start: 0.8832 (m-80) cc_final: 0.8475 (m-80)
REVERT: A  772 CYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6800 (t)
REVERT: B  845 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8150 (mtp)
REVERT: B  848 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7328 (m-40)
  outliers start: 21
  outliers final: 11
  residues processed: 71
  average time/residue: 0.1983
  time to fit residues: 18.4560
Evaluate side-chains
  60 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
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  690 LEU
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  845 MET
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  850 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0470
   chunk 11 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0030
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.4088

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.130292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.094295 restraints weight = 6549.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 3.15
r_work: 0.3250 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4097  Z= 0.123
  Angle     :  0.580   6.363   5597  Z= 0.298
  Chirality :  0.046   0.189    628
  Planarity :  0.004   0.062    722
  Dihedral  :  6.886  59.690    724
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 15.53 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.36), residues: 492
  helix: -1.15 (0.77), residues: 38
  sheet: -2.04 (0.39), residues: 137
  loop : -2.00 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 796 
 HIS   0.005   0.001   HIS A 636 
 PHE   0.010   0.001   PHE A 537 
 TYR   0.007   0.001   TYR B 959 
 ARG   0.002   0.000   ARG A 692 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00453 (    9)
  link_NAG-ASN         : angle       1.62494 (   27)
  hydrogen bonds       : bond        0.03070 (   82)
  hydrogen bonds       : angle       5.83198 (  210)
  SS BOND              : bond        0.00397 (    8)
  SS BOND              : angle       1.80619 (   16)
  covalent geometry    : bond        0.00280 ( 4080)
  covalent geometry    : angle       0.56333 ( 5554)

*********************** 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
  72 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 53
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: A  636 HIS cc_start: 0.6768 (p90) cc_final: 0.6512 (p-80)
REVERT: A  639 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8580 (pt)
REVERT: A  679 ARG cc_start: 0.8189 (ptt90) cc_final: 0.7758 (ptt90)
REVERT: A  693 PHE cc_start: 0.8827 (m-80) cc_final: 0.8564 (m-80)
REVERT: A  700 HIS cc_start: 0.6099 (OUTLIER) cc_final: 0.4936 (p90)
REVERT: A  750 ILE cc_start: 0.8512 (mp) cc_final: 0.8201 (tt)
REVERT: A  772 CYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6895 (t)
REVERT: B  848 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7263 (m-40)
  outliers start: 19
  outliers final: 12
  residues processed: 68
  average time/residue: 0.1976
  time to fit residues: 16.6023
Evaluate side-chains
  63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
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  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  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  977 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 768 ASN
** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.127630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.091963 restraints weight = 6469.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 3.09
r_work: 0.3201 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.5118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4097  Z= 0.204
  Angle     :  0.621   6.097   5597  Z= 0.318
  Chirality :  0.047   0.192    628
  Planarity :  0.005   0.059    722
  Dihedral  :  7.218  59.831    724
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 16.24 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.36), residues: 492
  helix: -1.20 (0.77), residues: 38
  sheet: -2.12 (0.41), residues: 123
  loop : -1.92 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 796 
 HIS   0.006   0.001   HIS A 636 
 PHE   0.016   0.001   PHE A 681 
 TYR   0.016   0.002   TYR B 803 
 ARG   0.003   0.000   ARG A 692 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00391 (    9)
  link_NAG-ASN         : angle       1.79547 (   27)
  hydrogen bonds       : bond        0.03384 (   82)
  hydrogen bonds       : angle       5.96529 (  210)
  SS BOND              : bond        0.00442 (    8)
  SS BOND              : angle       1.91294 (   16)
  covalent geometry    : bond        0.00481 ( 4080)
  covalent geometry    : angle       0.60210 ( 5554)

*********************** 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
  71 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 50
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: A  570 GLU cc_start: 0.7253 (tp30) cc_final: 0.6946 (tp30)
REVERT: A  636 HIS cc_start: 0.6882 (p90) cc_final: 0.6643 (p90)
REVERT: A  639 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8576 (pt)
REVERT: A  648 PHE cc_start: 0.8653 (t80) cc_final: 0.8307 (t80)
REVERT: A  679 ARG cc_start: 0.8123 (ptt90) cc_final: 0.7750 (ptt90)
REVERT: A  693 PHE cc_start: 0.8836 (m-80) cc_final: 0.8561 (m-80)
REVERT: A  700 HIS cc_start: 0.6267 (OUTLIER) cc_final: 0.5387 (p90)
REVERT: A  750 ILE cc_start: 0.8532 (mp) cc_final: 0.8215 (tt)
REVERT: A  772 CYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6839 (t)
REVERT: B  803 TYR cc_start: 0.8407 (m-80) cc_final: 0.8144 (m-80)
REVERT: B  848 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7303 (m-40)
REVERT: B  884 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7731 (m-80)
  outliers start: 21
  outliers final: 12
  residues processed: 67
  average time/residue: 0.1801
  time to fit residues: 15.3581
Evaluate side-chains
  63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
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  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  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  977 CYS
Chi-restraints excluded: chain B residue  995 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    0.0980
   chunk 17 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.130359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.094936 restraints weight = 6428.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 3.05
r_work: 0.3254 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.5111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4097  Z= 0.125
  Angle     :  0.576   6.125   5597  Z= 0.295
  Chirality :  0.046   0.188    628
  Planarity :  0.004   0.055    722
  Dihedral  :  6.937  59.920    724
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 17.18 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.37), residues: 492
  helix: -1.00 (0.78), residues: 38
  sheet: -2.52 (0.38), residues: 148
  loop : -1.60 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 915 
 HIS   0.005   0.001   HIS A 636 
 PHE   0.013   0.001   PHE A 681 
 TYR   0.014   0.001   TYR B 803 
 ARG   0.002   0.000   ARG A 692 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00431 (    9)
  link_NAG-ASN         : angle       1.59551 (   27)
  hydrogen bonds       : bond        0.02877 (   82)
  hydrogen bonds       : angle       5.67161 (  210)
  SS BOND              : bond        0.00331 (    8)
  SS BOND              : angle       1.62535 (   16)
  covalent geometry    : bond        0.00287 ( 4080)
  covalent geometry    : angle       0.56119 ( 5554)

*********************** 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
  69 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  570 GLU cc_start: 0.7141 (tp30) cc_final: 0.6855 (tp30)
REVERT: A  636 HIS cc_start: 0.6690 (p90) cc_final: 0.6431 (p90)
REVERT: A  639 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8584 (pt)
REVERT: A  647 HIS cc_start: 0.6502 (m-70) cc_final: 0.6065 (m-70)
REVERT: A  648 PHE cc_start: 0.8597 (t80) cc_final: 0.8259 (t80)
REVERT: A  679 ARG cc_start: 0.8054 (ptt90) cc_final: 0.7655 (ptt90)
REVERT: A  693 PHE cc_start: 0.8877 (m-80) cc_final: 0.8611 (m-80)
REVERT: A  700 HIS cc_start: 0.6123 (OUTLIER) cc_final: 0.4988 (p90)
REVERT: A  750 ILE cc_start: 0.8593 (mp) cc_final: 0.8155 (tt)
REVERT: A  772 CYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6861 (t)
REVERT: B  803 TYR cc_start: 0.8420 (m-80) cc_final: 0.8141 (m-80)
REVERT: B  848 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.7275 (m-40)
REVERT: B  884 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7726 (m-80)
  outliers start: 17
  outliers final: 9
  residues processed: 67
  average time/residue: 0.1986
  time to fit residues: 16.8783
Evaluate side-chains
  62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
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  639 ILE
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 37 optimal weight:    0.0000
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0570
   chunk 30 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0770
   chunk 12 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0770
   chunk 19 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.1818

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

Flipped N/Q/H residues before XYZ refinement:
A 647 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.132313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.097496 restraints weight = 6293.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 3.03
r_work: 0.3300 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.5103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4097  Z= 0.108
  Angle     :  0.580   5.442   5597  Z= 0.300
  Chirality :  0.046   0.186    628
  Planarity :  0.004   0.053    722
  Dihedral  :  6.740  59.868    724
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.88 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.37), residues: 492
  helix: -0.95 (0.80), residues: 38
  sheet: -1.97 (0.39), residues: 147
  loop : -1.68 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 915 
 HIS   0.004   0.001   HIS A 636 
 PHE   0.016   0.001   PHE A 681 
 TYR   0.012   0.001   TYR B 803 
 ARG   0.003   0.000   ARG A 692 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00448 (    9)
  link_NAG-ASN         : angle       1.46907 (   27)
  hydrogen bonds       : bond        0.02680 (   82)
  hydrogen bonds       : angle       5.44274 (  210)
  SS BOND              : bond        0.00271 (    8)
  SS BOND              : angle       1.46057 (   16)
  covalent geometry    : bond        0.00234 ( 4080)
  covalent geometry    : angle       0.56798 ( 5554)

*********************** 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
  62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  570 GLU cc_start: 0.7108 (tp30) cc_final: 0.6868 (tp30)
REVERT: A  639 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8541 (pt)
REVERT: A  647 HIS cc_start: 0.6337 (m170) cc_final: 0.6029 (m-70)
REVERT: A  679 ARG cc_start: 0.8062 (ptt90) cc_final: 0.7636 (ptt90)
REVERT: A  693 PHE cc_start: 0.8856 (m-80) cc_final: 0.8579 (m-80)
REVERT: A  700 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.5331 (p90)
REVERT: A  705 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7272 (mp0)
REVERT: A  750 ILE cc_start: 0.8515 (mp) cc_final: 0.8212 (tt)
REVERT: A  772 CYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6821 (t)
REVERT: B  803 TYR cc_start: 0.8390 (m-80) cc_final: 0.8111 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 60
  average time/residue: 0.1547
  time to fit residues: 11.9615
Evaluate side-chains
  61 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
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  639 ILE
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 32 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.136669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.104396 restraints weight = 6458.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.60
r_work: 0.3524 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4097  Z= 0.207
  Angle     :  0.641   6.315   5597  Z= 0.330
  Chirality :  0.048   0.193    628
  Planarity :  0.005   0.056    722
  Dihedral  :  7.178  59.666    724
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.35 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.37), residues: 492
  helix: -0.96 (0.81), residues: 38
  sheet: -1.91 (0.41), residues: 130
  loop : -1.80 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 699 
 HIS   0.002   0.001   HIS A 647 
 PHE   0.013   0.002   PHE A 681 
 TYR   0.016   0.002   TYR B 959 
 ARG   0.003   0.000   ARG A 692 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00378 (    9)
  link_NAG-ASN         : angle       1.68052 (   27)
  hydrogen bonds       : bond        0.03216 (   82)
  hydrogen bonds       : angle       5.81329 (  210)
  SS BOND              : bond        0.00417 (    8)
  SS BOND              : angle       1.78974 (   16)
  covalent geometry    : bond        0.00493 ( 4080)
  covalent geometry    : angle       0.62575 ( 5554)

*********************** 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
  65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: A  647 HIS cc_start: 0.6187 (m170) cc_final: 0.5906 (m-70)
REVERT: A  648 PHE cc_start: 0.8538 (t80) cc_final: 0.8313 (t80)
REVERT: A  679 ARG cc_start: 0.7971 (ptt90) cc_final: 0.7657 (ptt90)
REVERT: A  693 PHE cc_start: 0.8599 (m-80) cc_final: 0.8348 (m-80)
REVERT: A  700 HIS cc_start: 0.6229 (OUTLIER) cc_final: 0.5360 (p90)
REVERT: A  705 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7511 (mp0)
REVERT: A  750 ILE cc_start: 0.8328 (mp) cc_final: 0.8023 (tt)
REVERT: B  803 TYR cc_start: 0.8301 (m-80) cc_final: 0.8079 (m-80)
  outliers start: 14
  outliers final: 9
  residues processed: 63
  average time/residue: 0.1876
  time to fit residues: 16.3570
Evaluate side-chains
  59 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  541 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 B residue  800 VAL
Chi-restraints excluded: chain B residue  810 CYS
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Chi-restraints excluded: chain B residue  995 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.138048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.106000 restraints weight = 6435.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.63
r_work: 0.3554 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.5438

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= 0.161
  Angle     :  0.649   6.982   5597  Z= 0.336
  Chirality :  0.047   0.223    628
  Planarity :  0.005   0.056    722
  Dihedral  :  6.766  59.567    721
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.16 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 19.53 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.37), residues: 492
  helix: -0.99 (0.80), residues: 38
  sheet: -2.07 (0.40), residues: 141
  loop : -1.71 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 796 
 HIS   0.004   0.001   HIS A 769 
 PHE   0.016   0.001   PHE A 681 
 TYR   0.013   0.001   TYR B 803 
 ARG   0.002   0.000   ARG A 692 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00654 (    9)
  link_NAG-ASN         : angle       1.85144 (   27)
  hydrogen bonds       : bond        0.03043 (   82)
  hydrogen bonds       : angle       5.78837 (  210)
  SS BOND              : bond        0.00383 (    8)
  SS BOND              : angle       2.08238 (   16)
  covalent geometry    : bond        0.00371 ( 4080)
  covalent geometry    : angle       0.62902 ( 5554)

********************** 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
  60 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
REVERT: A  647 HIS cc_start: 0.6096 (m170) cc_final: 0.5856 (m-70)
REVERT: A  693 PHE cc_start: 0.8524 (m-80) cc_final: 0.8308 (m-80)
REVERT: A  700 HIS cc_start: 0.6151 (OUTLIER) cc_final: 0.5347 (p90)
REVERT: A  705 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7551 (mp0)
REVERT: A  750 ILE cc_start: 0.8465 (mp) cc_final: 0.8091 (tt)
REVERT: B  803 TYR cc_start: 0.8277 (m-80) cc_final: 0.8068 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 59
  average time/residue: 0.1558
  time to fit residues: 12.4086
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  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  541 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  749 LEU
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  810 CYS
Chi-restraints excluded: chain B residue  848 ASN
Chi-restraints excluded: chain B residue  896 CYS
Chi-restraints excluded: chain B residue  977 CYS
Chi-restraints excluded: chain B residue  995 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 36 optimal weight:    0.4980
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4144 r_free = 0.4144 target = 0.139293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.107029 restraints weight = 6373.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.65
r_work: 0.3575 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.5470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4097  Z= 0.140
  Angle     :  0.628   7.250   5597  Z= 0.323
  Chirality :  0.047   0.257    628
  Planarity :  0.004   0.055    722
  Dihedral  :  6.750  59.261    721
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.53 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.37), residues: 492
  helix: -0.95 (0.80), residues: 38
  sheet: -1.99 (0.40), residues: 141
  loop : -1.69 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 915 
 HIS   0.005   0.001   HIS A 567 
 PHE   0.016   0.001   PHE A 681 
 TYR   0.012   0.002   TYR B 803 
 ARG   0.002   0.000   ARG A 692 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00958 (    9)
  link_NAG-ASN         : angle       2.19136 (   27)
  hydrogen bonds       : bond        0.02904 (   82)
  hydrogen bonds       : angle       5.62391 (  210)
  SS BOND              : bond        0.00344 (    8)
  SS BOND              : angle       1.90304 (   16)
  covalent geometry    : bond        0.00317 ( 4080)
  covalent geometry    : angle       0.60287 ( 5554)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3251.73 seconds
wall clock time: 58 minutes 54.62 seconds (3534.62 seconds total)