Starting phenix.real_space_refine
on Wed Feb  4 05:36:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9z5q_73821/02_2026/9z5q_73821.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9z5q_73821/02_2026/9z5q_73821.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9z5q_73821/02_2026/9z5q_73821.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9z5q_73821/02_2026/9z5q_73821.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9z5q_73821/02_2026/9z5q_73821.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9z5q_73821/02_2026/9z5q_73821.map"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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: 5
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    2846      2.51       5
     N     746      2.21       5
     O     816      1.98       5
     H    4286      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8716
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 1862
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "B"
      Number of atoms: 6854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 6854
          Classifications: {'peptide': 417}
          Link IDs: {'PTRANS': 23, 'TRANS': 393}
          Chain breaks: 1
  Time building chain proxies: 1.52, per 1000 atoms: 0.17
  Number of scatterers: 8716
  At special positions: 0
  Unit cell: (71.89, 79.079, 94.484, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     O     816      8.00
     N     746      7.00
     C    2846      6.00
     H    4286      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  95 " 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
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 161.7 milliseconds
  

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1002

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      40.1% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 86 through 90
    Processing helix  chain 'B' and resid 596 through 607
    Processing helix  chain 'B' and resid 623 through 625
      No H-bonds generated for 'chain 'B' and resid 623 through 625'
    Processing helix  chain 'B' and resid 626 through 637
      removed outlier: 3.880A  pdb=" N   GLU B 630 " --> pdb=" O   ASN B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 645
      removed outlier: 4.350A  pdb=" N   LEU B 644 " --> pdb=" O   ARG B 640 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LYS B 645 " --> pdb=" O   PRO B 641 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 640 through 645'
    Processing helix  chain 'B' and resid 654 through 656
      No H-bonds generated for 'chain 'B' and resid 654 through 656'
    Processing helix  chain 'B' and resid 662 through 676
    Processing helix  chain 'B' and resid 677 through 681
    Processing helix  chain 'B' and resid 698 through 703
      removed outlier: 3.500A  pdb=" N   CYS B 702 " --> pdb=" O   ASN B 698 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 724
    Processing helix  chain 'B' and resid 732 through 741
      removed outlier: 3.650A  pdb=" N   TYR B 736 " --> pdb=" O   ILE B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 748 through 753
      removed outlier: 4.114A  pdb=" N   VAL B 752 " --> pdb=" O   ASP B 748 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 753 through 766
    Processing helix  chain 'B' and resid 803 through 816
    Processing helix  chain 'B' and resid 816 through 833
      removed outlier: 4.818A  pdb=" N   LYS B 822 " --> pdb=" O   ASN B 818 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   GLN B 823 " --> pdb=" O   ARG B 819 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU B 833 " --> pdb=" O   GLU B 829 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 836 through 841
      removed outlier: 3.901A  pdb=" N   ILE B 840 " --> pdb=" O   PRO B 836 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 844 through 854
    Processing helix  chain 'B' and resid 859 through 866
    Processing helix  chain 'B' and resid 877 through 890
    Processing helix  chain 'B' and resid 891 through 903
    Processing helix  chain 'B' and resid 953 through 967
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7
      removed outlier: 3.616A  pdb=" N   VAL A  78 " --> pdb=" O   CYS A  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13
      removed outlier: 7.180A  pdb=" N   VAL A  12 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59
      removed outlier: 6.549A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   GLY A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   MET A  34 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   ILE A  98 " --> pdb=" O   TRP A  32 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   MET A  34 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ALA A  96 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   TRP A  36 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   TYR A  94 " --> pdb=" O   TRP A  36 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   ARG A  38 " --> pdb=" O   VAL A  92 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   VAL A  92 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 59
      removed outlier: 6.549A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   GLY A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   MET A  34 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   ILE A  98 " --> pdb=" O   TRP A  32 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   MET A  34 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ALA A  96 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   TRP A  36 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   TYR A  94 " --> pdb=" O   TRP A  36 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   ARG A  38 " --> pdb=" O   VAL A  92 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   VAL A  92 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 554 through 558
    Processing sheet with id=AA6, first strand: chain 'B' and resid 617 through 622
      removed outlier: 3.758A  pdb=" N   LEU B 622 " --> pdb=" O   GLU B 651 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 683 through 685
    Processing sheet with id=AA8, first strand: chain 'B' and resid 776 through 779
      removed outlier: 3.854A  pdb=" N   TYR B 786 " --> pdb=" O   GLU B 779 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 867 through 870
      removed outlier: 3.690A  pdb=" N   ILE B 927 " --> pdb=" O   ILE B 868 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   THR B 926 " --> pdb=" O   LEU B 946 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   LEU B 948 " --> pdb=" O   THR B 926 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   GLU B 928 " --> pdb=" O   LEU B 948 " (cutoff:3.500A)

    187 hydrogen bonds defined for protein.
    525 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: 2.02

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4046
        1.03 -     1.23: 246
        1.23 -     1.42: 1998
        1.42 -     1.62: 2508
        1.62 -     1.81: 37
  Bond restraints: 8835
  Sorted by residual:
  bond pdb=" N   ASN A  83 "
       pdb=" H   ASN A  83 "
    ideal  model  delta    sigma   weight residual
    0.860  1.038 -0.178 2.00e-02 2.50e+03 7.90e+01
  bond pdb=" N   LEU A  85 "
       pdb=" H   LEU A  85 "
    ideal  model  delta    sigma   weight residual
    0.860  1.037 -0.177 2.00e-02 2.50e+03 7.81e+01
  bond pdb=" N   VAL A 118 "
       pdb=" H   VAL A 118 "
    ideal  model  delta    sigma   weight residual
    0.860  1.037 -0.177 2.00e-02 2.50e+03 7.80e+01
  bond pdb=" N   SER A  21 "
       pdb=" H   SER A  21 "
    ideal  model  delta    sigma   weight residual
    0.860  1.037 -0.177 2.00e-02 2.50e+03 7.79e+01
  bond pdb=" N   SER A   7 "
       pdb=" H   SER A   7 "
    ideal  model  delta    sigma   weight residual
    0.860  1.036 -0.176 2.00e-02 2.50e+03 7.78e+01
  ... (remaining 8830 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 15036
        1.25 -     2.49: 722
        2.49 -     3.74: 103
        3.74 -     4.98: 32
        4.98 -     6.23: 6
  Bond angle restraints: 15899
  Sorted by residual:
  angle pdb=" N   GLY A  15 "
        pdb=" CA  GLY A  15 "
        pdb=" C   GLY A  15 "
      ideal   model   delta    sigma   weight residual
     115.36  109.46    5.90 1.33e+00 5.65e-01 1.97e+01
  angle pdb=" N   GLU A  88 "
        pdb=" CA  GLU A  88 "
        pdb=" C   GLU A  88 "
      ideal   model   delta    sigma   weight residual
     111.28  106.51    4.77 1.09e+00 8.42e-01 1.92e+01
  angle pdb=" C   ALA A  91 "
        pdb=" N   VAL A  92 "
        pdb=" CA  VAL A  92 "
      ideal   model   delta    sigma   weight residual
     122.37  127.88   -5.51 1.29e+00 6.01e-01 1.82e+01
  angle pdb=" CA  ARG A  66 "
        pdb=" C   ARG A  66 "
        pdb=" O   ARG A  66 "
      ideal   model   delta    sigma   weight residual
     120.55  116.43    4.12 1.06e+00 8.90e-01 1.51e+01
  angle pdb=" CA  PHE A  67 "
        pdb=" CB  PHE A  67 "
        pdb=" CG  PHE A  67 "
      ideal   model   delta    sigma   weight residual
     113.80  117.64   -3.84 1.00e+00 1.00e+00 1.48e+01
  ... (remaining 15894 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 3585
       17.56 -    35.12: 399
       35.12 -    52.68: 142
       52.68 -    70.24: 41
       70.24 -    87.80: 13
  Dihedral angle restraints: 4180
    sinusoidal: 2232
      harmonic: 1948
  Sorted by residual:
  dihedral pdb=" CG  ARG A  45 "
           pdb=" CD  ARG A  45 "
           pdb=" NE  ARG A  45 "
           pdb=" CZ  ARG A  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.47   44.47     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CB  GLU B 577 "
           pdb=" CG  GLU B 577 "
           pdb=" CD  GLU B 577 "
           pdb=" OE1 GLU B 577 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.80   87.80     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CG  ARG B 895 "
           pdb=" CD  ARG B 895 "
           pdb=" NE  ARG B 895 "
           pdb=" CZ  ARG B 895 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.73   43.73     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 4177 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 510
       0.049 -    0.097: 93
       0.097 -    0.145: 22
       0.145 -    0.194: 7
       0.194 -    0.242: 2
  Chirality restraints: 634
  Sorted by residual:
  chirality pdb=" CA  VAL A 118 "
            pdb=" N   VAL A 118 "
            pdb=" C   VAL A 118 "
            pdb=" CB  VAL A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  LEU A  18 "
            pdb=" N   LEU A  18 "
            pdb=" C   LEU A  18 "
            pdb=" CB  LEU A  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.98e-01
  chirality pdb=" CA  LEU A  80 "
            pdb=" N   LEU A  80 "
            pdb=" C   LEU A  80 "
            pdb=" CB  LEU A  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.01e-01
  ... (remaining 631 not shown)

  Planarity restraints: 1310
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  83 "   -0.273 2.00e-02 2.50e+03   4.77e-01 3.41e+03
        pdb=" CG  ASN A  83 "    0.022 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  83 "    0.267 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  83 "    0.003 2.00e-02 2.50e+03
        pdb="HD21 ASN A  83 "    0.771 2.00e-02 2.50e+03
        pdb="HD22 ASN A  83 "   -0.789 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A  81 "    0.333 2.00e-02 2.50e+03   3.67e-01 2.03e+03
        pdb=" CD  GLN A  81 "   -0.025 2.00e-02 2.50e+03
        pdb=" OE1 GLN A  81 "   -0.319 2.00e-02 2.50e+03
        pdb=" NE2 GLN A  81 "   -0.003 2.00e-02 2.50e+03
        pdb="HE21 GLN A  81 "    0.553 2.00e-02 2.50e+03
        pdb="HE22 GLN A  81 "   -0.539 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 117 "    0.174 2.00e-02 2.50e+03   1.67e-01 4.21e+02
        pdb=" CD  GLN A 117 "   -0.017 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 117 "   -0.162 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 117 "   -0.005 2.00e-02 2.50e+03
        pdb="HE21 GLN A 117 "   -0.231 2.00e-02 2.50e+03
        pdb="HE22 GLN A 117 "    0.241 2.00e-02 2.50e+03
  ... (remaining 1307 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 736
        2.21 -     2.80: 17863
        2.80 -     3.40: 24246
        3.40 -     4.00: 32784
        4.00 -     4.60: 49600
  Nonbonded interactions: 125229
  Sorted by model distance:
  nonbonded pdb=" HE1 TRP A  32 "
            pdb=" O   LEU B 790 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" OE1 GLU B 555 "
            pdb="HH21 ARG B 557 "
     model   vdw
     1.665 2.450
  nonbonded pdb="HH11 ARG B 595 "
            pdb=" OE2 GLU B 847 "
     model   vdw
     1.667 2.450
  nonbonded pdb=" OD2 ASP B 578 "
            pdb="HH21 ARG B 580 "
     model   vdw
     1.686 2.450
  nonbonded pdb=" HH  TYR A  33 "
            pdb=" OE2 GLU B 806 "
     model   vdw
     1.686 2.450
  ... (remaining 125224 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:             1.710
  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:             0.060
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.360
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4550  Z= 0.258
  Angle     :  0.703   6.230   6160  Z= 0.445
  Chirality :  0.045   0.242    634
  Planarity :  0.004   0.044    800
  Dihedral  : 18.850  87.801   1685
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.63 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 27.67 %
    Favored  : 66.25 %
  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:  0.37 (0.36), residues: 533
  helix:  1.18 (0.38), residues: 183
  sheet: -0.62 (0.52), residues: 103
  loop :  0.07 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  19 
 TYR   0.007   0.001   TYR B 736 
 PHE   0.007   0.001   PHE A  47 
 TRP   0.017   0.001   TRP B 649 
 HIS   0.002   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 4549)
  covalent geometry    : angle       0.70352 ( 6158)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.57919 (    2)
  hydrogen bonds       : bond        0.13558 (  181)
  hydrogen bonds       : angle       6.60760 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 ILE cc_start: 0.4442 (OUTLIER) cc_final: 0.3977 (pp)
REVERT: B  557 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7815 (mtt180)
REVERT: B  633 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7177 (mtm-85)
REVERT: B  647 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7208 (ttm-80)
REVERT: B  805 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7580 (mtt90)
REVERT: B  945 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7814 (ttm-80)
  outliers start: 29
  outliers final: 19
  residues processed: 101
  average time/residue: 0.2407
  time to fit residues: 28.1310
Evaluate side-chains
  96 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  599 GLN
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  633 ARG
Chi-restraints excluded: chain B residue  647 ARG
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  789 ASP
Chi-restraints excluded: chain B residue  805 ARG
Chi-restraints excluded: chain B residue  835 LEU
Chi-restraints excluded: chain B residue  890 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0770
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.173831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.139511 restraints weight = 14856.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.59
r_work: 0.3385 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.0746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4550  Z= 0.138
  Angle     :  0.531   4.413   6160  Z= 0.279
  Chirality :  0.038   0.137    634
  Planarity :  0.004   0.031    800
  Dihedral  :  8.962  50.987    655
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 28.30 %
    Favored  : 66.67 %
  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:  0.41 (0.36), residues: 533
  helix:  1.28 (0.38), residues: 183
  sheet: -0.72 (0.53), residues: 103
  loop :  0.09 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 665 
 TYR   0.008   0.001   TYR A  53 
 PHE   0.014   0.001   PHE A  47 
 TRP   0.007   0.001   TRP A  32 
 HIS   0.004   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4549)
  covalent geometry    : angle       0.53068 ( 6158)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       0.46354 (    2)
  hydrogen bonds       : bond        0.04134 (  181)
  hydrogen bonds       : angle       5.17418 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 ILE cc_start: 0.4501 (OUTLIER) cc_final: 0.3930 (pp)
REVERT: A   64 LYS cc_start: 0.8587 (tttm) cc_final: 0.7982 (ttmt)
REVERT: B  557 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7874 (mtt180)
REVERT: B  871 ASN cc_start: 0.7437 (t0) cc_final: 0.6790 (t0)
REVERT: B  945 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7829 (ttm-80)
  outliers start: 24
  outliers final: 18
  residues processed: 93
  average time/residue: 0.1872
  time to fit residues: 20.9512
Evaluate side-chains
  92 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  599 GLN
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  617 ARG
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  932 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
B 871 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.171349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.137362 restraints weight = 14604.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.54
r_work: 0.3372 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4550  Z= 0.161
  Angle     :  0.517   4.347   6160  Z= 0.271
  Chirality :  0.038   0.129    634
  Planarity :  0.004   0.030    800
  Dihedral  :  7.484  51.370    633
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 26.83 %
    Favored  : 67.92 %
  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:  0.32 (0.36), residues: 533
  helix:  1.21 (0.38), residues: 184
  sheet: -0.76 (0.54), residues: 101
  loop :  0.03 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  19 
 TYR   0.009   0.001   TYR A  53 
 PHE   0.017   0.001   PHE B 954 
 TRP   0.007   0.001   TRP A  36 
 HIS   0.004   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4549)
  covalent geometry    : angle       0.51707 ( 6158)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       0.57761 (    2)
  hydrogen bonds       : bond        0.03883 (  181)
  hydrogen bonds       : angle       4.89649 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 ILE cc_start: 0.4476 (OUTLIER) cc_final: 0.3976 (pp)
REVERT: B  557 ARG cc_start: 0.8116 (ttm170) cc_final: 0.7774 (mtt180)
REVERT: B  733 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8005 (tpm170)
REVERT: B  871 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7042 (t0)
REVERT: B  945 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7839 (ttm-80)
  outliers start: 25
  outliers final: 20
  residues processed: 90
  average time/residue: 0.1860
  time to fit residues: 20.3382
Evaluate side-chains
  95 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLN
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  599 GLN
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  617 ARG
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  789 ASP
Chi-restraints excluded: chain B residue  835 LEU
Chi-restraints excluded: chain B residue  871 ASN
Chi-restraints excluded: chain B residue  874 CYS
Chi-restraints excluded: chain B residue  888 LEU
Chi-restraints excluded: chain B residue  932 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 15 optimal weight:    0.0010
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.3980
   chunk 37 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.5386

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.169677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.132686 restraints weight = 14825.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.46
r_work: 0.3380 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4550  Z= 0.128
  Angle     :  0.498   4.274   6160  Z= 0.261
  Chirality :  0.038   0.129    634
  Planarity :  0.004   0.030    800
  Dihedral  :  7.259  51.525    630
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 27.04 %
    Favored  : 67.92 %
  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:  0.35 (0.36), residues: 533
  helix:  1.25 (0.38), residues: 184
  sheet: -0.58 (0.54), residues: 99
  loop : -0.07 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  19 
 TYR   0.010   0.001   TYR B 873 
 PHE   0.019   0.001   PHE B 954 
 TRP   0.007   0.001   TRP A  32 
 HIS   0.003   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4549)
  covalent geometry    : angle       0.49826 ( 6158)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       0.39878 (    2)
  hydrogen bonds       : bond        0.03589 (  181)
  hydrogen bonds       : angle       4.75275 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7650 (tt0)
REVERT: A   28 ILE cc_start: 0.4455 (OUTLIER) cc_final: 0.3976 (pp)
REVERT: B  557 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7782 (mtt180)
REVERT: B  633 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7292 (mtm-85)
REVERT: B  945 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7840 (ttm-80)
REVERT: B  954 PHE cc_start: 0.8274 (t80) cc_final: 0.8017 (t80)
  outliers start: 24
  outliers final: 20
  residues processed: 91
  average time/residue: 0.1919
  time to fit residues: 20.9324
Evaluate side-chains
  93 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue    5 GLN
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  599 GLN
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  617 ARG
Chi-restraints excluded: chain B residue  633 ARG
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  789 ASP
Chi-restraints excluded: chain B residue  835 LEU
Chi-restraints excluded: chain B residue  874 CYS
Chi-restraints excluded: chain B residue  932 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0050
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 4 optimal weight:    0.1980
   chunk 36 optimal weight:    0.1980
   overall best weight:    0.3594

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.170948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.134178 restraints weight = 14689.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.47
r_work: 0.3398 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4550  Z= 0.100
  Angle     :  0.473   4.389   6160  Z= 0.244
  Chirality :  0.038   0.131    634
  Planarity :  0.003   0.029    800
  Dihedral  :  7.065  52.026    629
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 26.83 %
    Favored  : 68.34 %
  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:  0.39 (0.36), residues: 533
  helix:  1.21 (0.37), residues: 191
  sheet: -0.35 (0.55), residues: 95
  loop : -0.13 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  19 
 TYR   0.009   0.001   TYR A  37 
 PHE   0.011   0.001   PHE A  47 
 TRP   0.007   0.001   TRP A  32 
 HIS   0.003   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 4549)
  covalent geometry    : angle       0.47317 ( 6158)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.31570 (    2)
  hydrogen bonds       : bond        0.03203 (  181)
  hydrogen bonds       : angle       4.49750 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7662 (tt0)
REVERT: A   28 ILE cc_start: 0.4483 (OUTLIER) cc_final: 0.4039 (pp)
REVERT: B  557 ARG cc_start: 0.7979 (ttm170) cc_final: 0.7765 (mtt180)
REVERT: B  572 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7149 (mmtp)
REVERT: B  609 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7174 (mttm)
REVERT: B  633 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7162 (mtm-85)
REVERT: B  945 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7800 (ttm-80)
  outliers start: 23
  outliers final: 18
  residues processed: 95
  average time/residue: 0.2004
  time to fit residues: 22.7978
Evaluate side-chains
  93 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  572 LYS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  599 GLN
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  617 ARG
Chi-restraints excluded: chain B residue  633 ARG
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  789 ASP
Chi-restraints excluded: chain B residue  835 LEU
Chi-restraints excluded: chain B residue  874 CYS
Chi-restraints excluded: chain B residue  932 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 3 optimal weight:    0.2980
   chunk 34 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 801 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.174754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.134406 restraints weight = 14735.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.70
r_work: 0.3373 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4550  Z= 0.114
  Angle     :  0.473   4.275   6160  Z= 0.244
  Chirality :  0.038   0.129    634
  Planarity :  0.003   0.028    800
  Dihedral  :  7.027  52.719    629
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 25.16 %
    Favored  : 68.55 %
  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:  0.39 (0.36), residues: 533
  helix:  1.24 (0.37), residues: 191
  sheet: -0.41 (0.55), residues: 95
  loop : -0.13 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  19 
 TYR   0.008   0.001   TYR A  37 
 PHE   0.013   0.001   PHE A  47 
 TRP   0.006   0.001   TRP A  32 
 HIS   0.002   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4549)
  covalent geometry    : angle       0.47302 ( 6158)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       0.36571 (    2)
  hydrogen bonds       : bond        0.03196 (  181)
  hydrogen bonds       : angle       4.45614 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 71
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7611 (tt0)
REVERT: A   28 ILE cc_start: 0.4480 (OUTLIER) cc_final: 0.4054 (pp)
REVERT: B  572 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7279 (mmtp)
REVERT: B  609 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7173 (mttm)
REVERT: B  633 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7143 (mtm-85)
REVERT: B  733 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7930 (tpm170)
REVERT: B  803 ASN cc_start: 0.7440 (m-40) cc_final: 0.7157 (m110)
REVERT: B  945 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7649 (ttm-80)
REVERT: B  954 PHE cc_start: 0.8481 (t80) cc_final: 0.8169 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 94
  average time/residue: 0.1606
  time to fit residues: 18.4570
Evaluate side-chains
  96 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue    5 GLN
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  572 LYS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  599 GLN
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  617 ARG
Chi-restraints excluded: chain B residue  633 ARG
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  691 TYR
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  789 ASP
Chi-restraints excluded: chain B residue  798 MET
Chi-restraints excluded: chain B residue  835 LEU
Chi-restraints excluded: chain B residue  874 CYS
Chi-restraints excluded: chain B residue  932 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 7 optimal weight:    0.1980
   chunk 10 optimal weight:    0.0980
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.3380

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.174045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.140431 restraints weight = 14852.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.53
r_work: 0.3422 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4550  Z= 0.096
  Angle     :  0.466   4.403   6160  Z= 0.238
  Chirality :  0.038   0.132    634
  Planarity :  0.003   0.028    800
  Dihedral  :  6.940  52.963    629
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 24.95 %
    Favored  : 68.97 %
  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:  0.49 (0.36), residues: 533
  helix:  1.30 (0.37), residues: 191
  sheet: -0.33 (0.55), residues: 95
  loop : -0.06 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  19 
 TYR   0.009   0.001   TYR A  37 
 PHE   0.011   0.001   PHE A  47 
 TRP   0.006   0.001   TRP A  32 
 HIS   0.002   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 4549)
  covalent geometry    : angle       0.46601 ( 6158)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.27227 (    2)
  hydrogen bonds       : bond        0.03060 (  181)
  hydrogen bonds       : angle       4.33762 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 70
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7751 (tt0)
REVERT: A   28 ILE cc_start: 0.4523 (OUTLIER) cc_final: 0.4099 (pp)
REVERT: B  609 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7152 (mttm)
REVERT: B  633 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7219 (mtm-85)
REVERT: B  647 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7117 (ttm-80)
REVERT: B  733 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8020 (tpm170)
REVERT: B  803 ASN cc_start: 0.7597 (m-40) cc_final: 0.7355 (m-40)
REVERT: B  954 PHE cc_start: 0.8476 (t80) cc_final: 0.8127 (t80)
  outliers start: 29
  outliers final: 21
  residues processed: 92
  average time/residue: 0.1962
  time to fit residues: 21.3514
Evaluate side-chains
  95 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  599 GLN
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  617 ARG
Chi-restraints excluded: chain B residue  633 ARG
Chi-restraints excluded: chain B residue  647 ARG
Chi-restraints excluded: chain B residue  691 TYR
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  778 ASP
Chi-restraints excluded: chain B residue  789 ASP
Chi-restraints excluded: chain B residue  798 MET
Chi-restraints excluded: chain B residue  835 LEU
Chi-restraints excluded: chain B residue  874 CYS
Chi-restraints excluded: chain B residue  932 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0370
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.170130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.133012 restraints weight = 14632.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 2.47
r_work: 0.3381 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4550  Z= 0.133
  Angle     :  0.480   4.273   6160  Z= 0.249
  Chirality :  0.038   0.129    634
  Planarity :  0.003   0.032    800
  Dihedral  :  6.947  53.721    629
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 24.32 %
    Favored  : 69.60 %
  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:  0.44 (0.36), residues: 533
  helix:  1.28 (0.38), residues: 191
  sheet: -0.41 (0.54), residues: 95
  loop : -0.09 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 624 
 TYR   0.007   0.001   TYR A  37 
 PHE   0.014   0.001   PHE A  47 
 TRP   0.006   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4549)
  covalent geometry    : angle       0.48035 ( 6158)
  SS BOND              : bond        0.00116 (    1)
  SS BOND              : angle       0.38530 (    2)
  hydrogen bonds       : bond        0.03186 (  181)
  hydrogen bonds       : angle       4.43690 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7793 (tt0)
REVERT: A   28 ILE cc_start: 0.4469 (OUTLIER) cc_final: 0.4084 (pp)
REVERT: B  609 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7158 (mttm)
REVERT: B  633 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7275 (mtm-85)
REVERT: B  647 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7191 (ttm-80)
REVERT: B  733 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8080 (tpm170)
REVERT: B  803 ASN cc_start: 0.7677 (m-40) cc_final: 0.7438 (m110)
REVERT: B  871 ASN cc_start: 0.7828 (t0) cc_final: 0.7141 (t0)
REVERT: B  954 PHE cc_start: 0.8488 (t80) cc_final: 0.8198 (t80)
  outliers start: 29
  outliers final: 21
  residues processed: 94
  average time/residue: 0.1905
  time to fit residues: 21.5674
Evaluate side-chains
  99 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  599 GLN
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  617 ARG
Chi-restraints excluded: chain B residue  633 ARG
Chi-restraints excluded: chain B residue  647 ARG
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  778 ASP
Chi-restraints excluded: chain B residue  789 ASP
Chi-restraints excluded: chain B residue  798 MET
Chi-restraints excluded: chain B residue  835 LEU
Chi-restraints excluded: chain B residue  874 CYS
Chi-restraints excluded: chain B residue  932 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0050
   chunk 52 optimal weight:    0.0010
   chunk 48 optimal weight:    0.1980
   chunk 12 optimal weight:    0.0870
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   overall best weight:    0.1178

-------------------------------------------------------------------------------
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 = 0.4048 r_free = 0.4048 target = 0.177245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.142268 restraints weight = 14571.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.67
r_work: 0.3407 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4550  Z= 0.084
  Angle     :  0.462   4.704   6160  Z= 0.235
  Chirality :  0.038   0.136    634
  Planarity :  0.003   0.027    800
  Dihedral  :  6.788  53.827    629
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 25.16 %
    Favored  : 70.65 %
  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:  0.90 (0.38), residues: 533
  helix:  1.62 (0.38), residues: 183
  sheet: -0.29 (0.52), residues: 107
  loop :  0.37 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  19 
 TYR   0.009   0.001   TYR A  37 
 PHE   0.010   0.001   PHE A  47 
 TRP   0.007   0.001   TRP B 649 
 HIS   0.002   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 4549)
  covalent geometry    : angle       0.46175 ( 6158)
  SS BOND              : bond        0.00018 (    1)
  SS BOND              : angle       0.09711 (    2)
  hydrogen bonds       : bond        0.02888 (  181)
  hydrogen bonds       : angle       4.21369 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7616 (tt0)
REVERT: A   28 ILE cc_start: 0.4370 (OUTLIER) cc_final: 0.3965 (pp)
REVERT: B  609 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7187 (mttm)
REVERT: B  633 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7272 (mtm-85)
REVERT: B  647 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7034 (ttm-80)
REVERT: B  733 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7984 (tpm170)
REVERT: B  803 ASN cc_start: 0.7224 (m-40) cc_final: 0.7015 (m-40)
REVERT: B  871 ASN cc_start: 0.7814 (t0) cc_final: 0.7114 (t0)
REVERT: B  942 CYS cc_start: 0.8240 (m) cc_final: 0.7945 (m)
REVERT: B  954 PHE cc_start: 0.8408 (t80) cc_final: 0.8173 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 91
  average time/residue: 0.1787
  time to fit residues: 19.4815
Evaluate side-chains
  89 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  617 ARG
Chi-restraints excluded: chain B residue  633 ARG
Chi-restraints excluded: chain B residue  647 ARG
Chi-restraints excluded: chain B residue  691 TYR
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  835 LEU
Chi-restraints excluded: chain B residue  874 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    0.0070
   chunk 27 optimal weight:    0.0050
   chunk 25 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0030
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.3422

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.174135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.141199 restraints weight = 14728.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.46
r_work: 0.3435 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4550  Z= 0.099
  Angle     :  0.470   4.505   6160  Z= 0.241
  Chirality :  0.038   0.130    634
  Planarity :  0.003   0.027    800
  Dihedral  :  6.341  44.935    626
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 25.37 %
    Favored  : 70.65 %
  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:  0.93 (0.38), residues: 533
  helix:  1.70 (0.38), residues: 183
  sheet: -0.32 (0.52), residues: 107
  loop :  0.37 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 624 
 TYR   0.009   0.001   TYR A  37 
 PHE   0.012   0.001   PHE A  47 
 TRP   0.005   0.001   TRP B 884 
 HIS   0.002   0.001   HIS B 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 4549)
  covalent geometry    : angle       0.46992 ( 6158)
  SS BOND              : bond        0.00112 (    1)
  SS BOND              : angle       0.31345 (    2)
  hydrogen bonds       : bond        0.02953 (  181)
  hydrogen bonds       : angle       4.22615 (  525)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7787 (tt0)
REVERT: A   28 ILE cc_start: 0.4324 (OUTLIER) cc_final: 0.3926 (pp)
REVERT: B  609 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7145 (mttm)
REVERT: B  633 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7310 (mtm-85)
REVERT: B  647 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7047 (ttm-80)
REVERT: B  733 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8193 (tpm170)
REVERT: B  803 ASN cc_start: 0.7353 (m-40) cc_final: 0.7141 (m-40)
REVERT: B  871 ASN cc_start: 0.7799 (t0) cc_final: 0.7100 (t0)
REVERT: B  942 CYS cc_start: 0.8458 (m) cc_final: 0.8150 (m)
REVERT: B  945 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7769 (ttm-80)
REVERT: B  954 PHE cc_start: 0.8395 (t80) cc_final: 0.8179 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1990
  time to fit residues: 20.4957
Evaluate side-chains
  93 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain B residue  559 HIS
Chi-restraints excluded: chain B residue  598 LYS
Chi-restraints excluded: chain B residue  609 LYS
Chi-restraints excluded: chain B residue  617 ARG
Chi-restraints excluded: chain B residue  633 ARG
Chi-restraints excluded: chain B residue  647 ARG
Chi-restraints excluded: chain B residue  691 TYR
Chi-restraints excluded: chain B residue  733 ARG
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  835 LEU
Chi-restraints excluded: chain B residue  874 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0060
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.6996

-------------------------------------------------------------------------------
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 = 0.3986 r_free = 0.3986 target = 0.171154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.133898 restraints weight = 14582.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.47
r_work: 0.3373 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4550  Z= 0.138
  Angle     :  0.485   4.611   6160  Z= 0.250
  Chirality :  0.038   0.130    634
  Planarity :  0.003   0.028    800
  Dihedral  :  6.400  44.696    626
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 25.16 %
    Favored  : 70.65 %
  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:  0.52 (0.36), residues: 533
  helix:  1.36 (0.38), residues: 191
  sheet: -0.35 (0.53), residues: 95
  loop : -0.07 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 624 
 TYR   0.008   0.001   TYR A  37 
 PHE   0.014   0.001   PHE A  47 
 TRP   0.008   0.001   TRP B 814 
 HIS   0.002   0.001   HIS B 569 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4549)
  covalent geometry    : angle       0.48535 ( 6158)
  SS BOND              : bond        0.00103 (    1)
  SS BOND              : angle       0.49966 (    2)
  hydrogen bonds       : bond        0.03127 (  181)
  hydrogen bonds       : angle       4.34503 (  525)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2788.93 seconds
wall clock time: 47 minutes 49.13 seconds (2869.13 seconds total)