Starting phenix.real_space_refine
on Tue Mar  3 12:28:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lkh_23408/03_2026/7lkh_23408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lkh_23408/03_2026/7lkh_23408.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lkh_23408/03_2026/7lkh_23408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lkh_23408/03_2026/7lkh_23408.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lkh_23408/03_2026/7lkh_23408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lkh_23408/03_2026/7lkh_23408.map"
  }
  resolution = 3.5
  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=   0.005
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       8      5.16       5
     C    2661      2.51       5
     N     717      2.21       5
     O     793      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4179
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2338
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2338
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 22, 'TRANS': 263}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 959
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 854
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.07, per 1000 atoms: 0.26
  Number of scatterers: 4179
  At special positions: 0
  Unit cell: (70.2, 100.44, 88.56, 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       8     16.00
     O     793      8.00
     N     717      7.00
     C    2661      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 147 " - pdb=" SG  CYS A 169 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 667 "
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 165.6 milliseconds
  

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  976

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 8 sheets defined
      25.6% alpha, 29.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 110 through 114
    Processing helix  chain 'A' and resid 115 through 121
      removed outlier: 3.667A  pdb=" N   ARG A 121 " --> pdb=" O   SER A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 142 through 146
    Processing helix  chain 'A' and resid 157 through 161
      removed outlier: 3.925A  pdb=" N   LEU A 160 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 179
    Processing helix  chain 'A' and resid 181 through 187
    Processing helix  chain 'A' and resid 190 through 197
    Processing helix  chain 'A' and resid 208 through 215
    Processing helix  chain 'A' and resid 244 through 259
    Processing helix  chain 'A' and resid 644 through 648
    Processing helix  chain 'A' and resid 649 through 654
    Processing helix  chain 'A' and resid 657 through 665
    Processing helix  chain 'A' and resid 688 through 695
    Processing helix  chain 'A' and resid 697 through 701
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.745A  pdb=" N   GLN H  65 " --> pdb=" O   PRO H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.765A  pdb=" N   ILE L  83 " --> pdb=" O   GLN L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64
      removed outlier: 6.711A  pdb=" N   VAL A  61 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   HIS A 273 " --> pdb=" O   VAL A  61 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASP A  63 " --> pdb=" O   HIS A 273 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   HIS A 275 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 64
      removed outlier: 6.711A  pdb=" N   VAL A  61 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   HIS A 273 " --> pdb=" O   VAL A  61 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASP A  63 " --> pdb=" O   HIS A 273 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   HIS A 275 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   ILE A 681 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   GLN A  95 " --> pdb=" O   ILE A 681 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   VAL A 683 " --> pdb=" O   GLN A  95 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   PHE A  97 " --> pdb=" O   VAL A 683 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   LEU A 685 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   LYS A  99 " --> pdb=" O   LEU A 685 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   LEU A 687 " --> pdb=" O   LYS A  99 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   THR A 101 " --> pdb=" O   LEU A 687 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.429A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ILE H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ARG H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.924A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)

    151 hydrogen bonds defined for protein.
    348 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: 0.59

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1333
        1.34 -     1.46: 1038
        1.46 -     1.58: 1904
        1.58 -     1.71: 0
        1.71 -     1.83: 9
  Bond restraints: 4284
  Sorted by residual:
  bond pdb=" N   VAL A  55 "
       pdb=" CA  VAL A  55 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.19e-02 7.06e+03 1.23e+01
  bond pdb=" N   THR A  59 "
       pdb=" CA  THR A  59 "
    ideal  model  delta    sigma   weight residual
    1.462  1.491 -0.029 8.50e-03 1.38e+04 1.19e+01
  bond pdb=" N   VAL A  61 "
       pdb=" CA  VAL A  61 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.32e-02 5.74e+03 6.85e+00
  bond pdb=" N   LYS A  62 "
       pdb=" CA  LYS A  62 "
    ideal  model  delta    sigma   weight residual
    1.453  1.485 -0.032 1.31e-02 5.83e+03 5.86e+00
  bond pdb=" N   GLY A  53 "
       pdb=" CA  GLY A  53 "
    ideal  model  delta    sigma   weight residual
    1.451  1.488 -0.037 1.60e-02 3.91e+03 5.31e+00
  ... (remaining 4279 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 5485
        1.82 -     3.65: 282
        3.65 -     5.47: 52
        5.47 -     7.29: 6
        7.29 -     9.12: 2
  Bond angle restraints: 5827
  Sorted by residual:
  angle pdb=" C   LEU L  94 "
        pdb=" N   PRO L  95 "
        pdb=" CA  PRO L  95 "
      ideal   model   delta    sigma   weight residual
     119.84  113.38    6.46 1.25e+00 6.40e-01 2.67e+01
  angle pdb=" C   ASP A  83 "
        pdb=" N   TRP A  84 "
        pdb=" CA  TRP A  84 "
      ideal   model   delta    sigma   weight residual
     121.54  130.66   -9.12 1.91e+00 2.74e-01 2.28e+01
  angle pdb=" CA  VAL A  61 "
        pdb=" C   VAL A  61 "
        pdb=" O   VAL A  61 "
      ideal   model   delta    sigma   weight residual
     121.59  117.51    4.08 1.03e+00 9.43e-01 1.57e+01
  angle pdb=" CA  LYS A  62 "
        pdb=" C   LYS A  62 "
        pdb=" O   LYS A  62 "
      ideal   model   delta    sigma   weight residual
     121.81  117.32    4.49 1.18e+00 7.18e-01 1.45e+01
  angle pdb=" CA  ARG A 673 "
        pdb=" C   ARG A 673 "
        pdb=" O   ARG A 673 "
      ideal   model   delta    sigma   weight residual
     121.60  117.02    4.58 1.21e+00 6.83e-01 1.43e+01
  ... (remaining 5822 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 2350
       16.91 -    33.81: 185
       33.81 -    50.71: 35
       50.71 -    67.62: 6
       67.62 -    84.52: 8
  Dihedral angle restraints: 2584
    sinusoidal: 1070
      harmonic: 1514
  Sorted by residual:
  dihedral pdb=" CA  THR L  93 "
           pdb=" C   THR L  93 "
           pdb=" N   LEU L  94 "
           pdb=" CA  LEU L  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.11  -27.89     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" CA  PRO A 155 "
           pdb=" C   PRO A 155 "
           pdb=" N   GLY A 156 "
           pdb=" CA  GLY A 156 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.17   24.83     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  ARG H  98 "
           pdb=" C   ARG H  98 "
           pdb=" N   TYR H  99 "
           pdb=" CA  TYR H  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.12   22.88     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 2581 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 421
       0.042 -    0.084: 140
       0.084 -    0.126: 65
       0.126 -    0.169: 19
       0.169 -    0.211: 3
  Chirality restraints: 648
  Sorted by residual:
  chirality pdb=" CA  LYS A 256 "
            pdb=" N   LYS A 256 "
            pdb=" C   LYS A 256 "
            pdb=" CB  LYS A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  PHE A  65 "
            pdb=" N   PHE A  65 "
            pdb=" C   PHE A  65 "
            pdb=" CB  PHE A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  ARG L  53 "
            pdb=" N   ARG L  53 "
            pdb=" C   ARG L  53 "
            pdb=" CB  ARG L  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.14e-01
  ... (remaining 645 not shown)

  Planarity restraints: 744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG H  40 "    0.074 5.00e-02 4.00e+02   1.12e-01 2.00e+01
        pdb=" N   PRO H  41 "   -0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO H  41 "    0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO H  41 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 154 "   -0.065 5.00e-02 4.00e+02   9.68e-02 1.50e+01
        pdb=" N   PRO A 155 "    0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO A 155 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 155 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  65 "   -0.038 5.00e-02 4.00e+02   5.74e-02 5.28e+00
        pdb=" N   PRO A  66 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 741 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 26
        2.50 -     3.10: 3058
        3.10 -     3.70: 5794
        3.70 -     4.30: 8688
        4.30 -     4.90: 14923
  Nonbonded interactions: 32489
  Sorted by model distance:
  nonbonded pdb=" O4  NAG B   1 "
            pdb=" O7  NAG B   2 "
     model   vdw
     1.903 3.040
  nonbonded pdb=" OD2 ASP H  73 "
            pdb=" OG  SER H  76 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" O   GLY A  87 "
            pdb=" OH  TYR A 674 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" O   ASN L  77 "
            pdb=" OD1 ASN L  77 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   PHE A 276 "
            pdb=" O   ALA A 671 "
     model   vdw
     2.276 3.040
  ... (remaining 32484 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 group one per residue
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:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.800
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
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      :  0.006   0.064   4289  Z= 0.294
  Angle     :  0.943   9.116   5839  Z= 0.565
  Chirality :  0.054   0.211    648
  Planarity :  0.007   0.112    743
  Dihedral  : 13.326  84.519   1599
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.43 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.99 (0.37), residues: 506
  helix: -0.11 (0.59), residues: 80
  sheet: -0.14 (0.39), residues: 171
  loop : -1.16 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 230 
 TYR   0.031   0.003   TYR A  64 
 PHE   0.037   0.003   PHE A  65 
 TRP   0.014   0.002   TRP H  47 
 HIS   0.004   0.001   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 ( 4284)
  covalent geometry    : angle       0.93829 ( 5827)
  SS BOND              : bond        0.00750 (    3)
  SS BOND              : angle       1.90820 (    6)
  hydrogen bonds       : bond        0.12001 (  141)
  hydrogen bonds       : angle       5.63991 (  348)
  link_BETA1-4         : bond        0.01006 (    1)
  link_BETA1-4         : angle       2.94743 (    3)
  link_NAG-ASN         : bond        0.01075 (    1)
  link_NAG-ASN         : angle       2.07839 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  138 SER cc_start: 0.8344 (t) cc_final: 0.8138 (t)
REVERT: L  108 ARG cc_start: 0.4258 (ppt170) cc_final: 0.4046 (ppt170)
  outliers start: 1
  outliers final: 1
  residues processed: 80
  average time/residue: 0.0875
  time to fit residues: 8.6151
Evaluate side-chains
  52 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN
A 167 HIS
** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  34 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.156895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.129943 restraints weight = 5610.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.133639 restraints weight = 3391.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.136008 restraints weight = 2466.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.137688 restraints weight = 1996.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.138644 restraints weight = 1724.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4289  Z= 0.187
  Angle     :  0.734  14.163   5839  Z= 0.362
  Chirality :  0.048   0.169    648
  Planarity :  0.006   0.072    743
  Dihedral  :  6.381  59.684    613
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  5.87 %
    Favored  : 91.74 %
  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: -0.54 (0.37), residues: 506
  helix:  0.17 (0.60), residues: 72
  sheet: -0.09 (0.38), residues: 165
  loop : -0.61 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 267 
 TYR   0.038   0.002   TYR H  99 
 PHE   0.013   0.002   PHE A 663 
 TRP   0.011   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 4284)
  covalent geometry    : angle       0.72946 ( 5827)
  SS BOND              : bond        0.00661 (    3)
  SS BOND              : angle       0.60183 (    6)
  hydrogen bonds       : bond        0.03734 (  141)
  hydrogen bonds       : angle       5.15568 (  348)
  link_BETA1-4         : bond        0.00409 (    1)
  link_BETA1-4         : angle       3.40498 (    3)
  link_NAG-ASN         : bond        0.01101 (    1)
  link_NAG-ASN         : angle       1.64932 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7399 (mttt) cc_final: 0.6506 (mppt)
REVERT: A  244 ASP cc_start: 0.7221 (t70) cc_final: 0.6819 (t70)
  outliers start: 11
  outliers final: 6
  residues processed: 75
  average time/residue: 0.0696
  time to fit residues: 6.6806
Evaluate side-chains
  58 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   52 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 39 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0670
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0570
   chunk 30 optimal weight:    0.9980
   chunk 41 optimal weight:   10.0000
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN
A 198 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.162613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.135225 restraints weight = 5588.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.139046 restraints weight = 3420.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.141549 restraints weight = 2481.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.143227 restraints weight = 2013.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.144240 restraints weight = 1735.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4289  Z= 0.116
  Angle     :  0.630  13.043   5839  Z= 0.306
  Chirality :  0.045   0.156    648
  Planarity :  0.005   0.052    743
  Dihedral  :  5.376  52.293    611
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  9.35 %
    Favored  : 88.91 %
  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: -0.17 (0.38), residues: 506
  helix:  0.61 (0.62), residues: 72
  sheet:  0.10 (0.39), residues: 167
  loop : -0.37 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 652 
 TYR   0.029   0.001   TYR H  99 
 PHE   0.007   0.001   PHE L  98 
 TRP   0.014   0.001   TRP A  84 
 HIS   0.004   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4284)
  covalent geometry    : angle       0.62657 ( 5827)
  SS BOND              : bond        0.00286 (    3)
  SS BOND              : angle       0.85096 (    6)
  hydrogen bonds       : bond        0.03026 (  141)
  hydrogen bonds       : angle       4.78397 (  348)
  link_BETA1-4         : bond        0.01119 (    1)
  link_BETA1-4         : angle       2.78402 (    3)
  link_NAG-ASN         : bond        0.00283 (    1)
  link_NAG-ASN         : angle       0.92569 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7428 (mttt) cc_final: 0.6753 (mppt)
REVERT: H   87 THR cc_start: 0.7890 (m) cc_final: 0.7357 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0656
  time to fit residues: 6.1269
Evaluate side-chains
  63 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    0.0970
   chunk 33 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0670
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0570
   chunk 15 optimal weight:    0.1980
   chunk 12 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.2034

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

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
H  55 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.166213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.139159 restraints weight = 5514.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.143004 restraints weight = 3362.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.145556 restraints weight = 2438.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.147190 restraints weight = 1964.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.148180 restraints weight = 1695.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4289  Z= 0.097
  Angle     :  0.597  12.024   5839  Z= 0.288
  Chirality :  0.043   0.143    648
  Planarity :  0.005   0.055    743
  Dihedral  :  4.647  42.543    611
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.87 %
    Favored  : 86.96 %
  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:  0.01 (0.38), residues: 506
  helix:  0.97 (0.63), residues: 73
  sheet:  0.20 (0.39), residues: 166
  loop : -0.32 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 267 
 TYR   0.023   0.001   TYR H  99 
 PHE   0.007   0.001   PHE L  98 
 TRP   0.012   0.001   TRP A  84 
 HIS   0.001   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 4284)
  covalent geometry    : angle       0.59477 ( 5827)
  SS BOND              : bond        0.00306 (    3)
  SS BOND              : angle       0.66044 (    6)
  hydrogen bonds       : bond        0.02617 (  141)
  hydrogen bonds       : angle       4.51705 (  348)
  link_BETA1-4         : bond        0.01086 (    1)
  link_BETA1-4         : angle       2.40030 (    3)
  link_NAG-ASN         : bond        0.00097 (    1)
  link_NAG-ASN         : angle       0.84281 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7316 (mttt) cc_final: 0.6684 (mppt)
REVERT: A  666 TYR cc_start: 0.8553 (m-80) cc_final: 0.8349 (m-80)
REVERT: H   99 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6099 (p90)
REVERT: L   77 ASN cc_start: 0.7666 (p0) cc_final: 0.7460 (p0)
  outliers start: 10
  outliers final: 7
  residues processed: 70
  average time/residue: 0.0605
  time to fit residues: 5.5487
Evaluate side-chains
  71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:    0.0050
   chunk 4 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.6594

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.161698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.134842 restraints weight = 5534.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.138622 restraints weight = 3363.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.141082 restraints weight = 2432.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.142558 restraints weight = 1963.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.143767 restraints weight = 1704.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4289  Z= 0.128
  Angle     :  0.600  12.352   5839  Z= 0.294
  Chirality :  0.044   0.157    648
  Planarity :  0.004   0.044    743
  Dihedral  :  4.525  36.422    611
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.30 %
    Favored  : 85.65 %
  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:  0.01 (0.39), residues: 506
  helix:  0.87 (0.62), residues: 73
  sheet:  0.19 (0.39), residues: 165
  loop : -0.27 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 267 
 TYR   0.025   0.002   TYR H  99 
 PHE   0.009   0.001   PHE A 663 
 TRP   0.009   0.001   TRP A  84 
 HIS   0.002   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4284)
  covalent geometry    : angle       0.59807 ( 5827)
  SS BOND              : bond        0.00347 (    3)
  SS BOND              : angle       0.62659 (    6)
  hydrogen bonds       : bond        0.03101 (  141)
  hydrogen bonds       : angle       4.47735 (  348)
  link_BETA1-4         : bond        0.01152 (    1)
  link_BETA1-4         : angle       2.11932 (    3)
  link_NAG-ASN         : bond        0.00444 (    1)
  link_NAG-ASN         : angle       1.05201 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7448 (mttt) cc_final: 0.6635 (mppt)
REVERT: H   91 THR cc_start: 0.8841 (m) cc_final: 0.8378 (p)
REVERT: L   28 ASP cc_start: 0.7944 (p0) cc_final: 0.7704 (p0)
REVERT: L   73 LEU cc_start: 0.8711 (tt) cc_final: 0.8501 (tp)
REVERT: L   77 ASN cc_start: 0.7600 (p0) cc_final: 0.7385 (p0)
  outliers start: 14
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0613
  time to fit residues: 6.3878
Evaluate side-chains
  72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   93 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0870
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 180 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.160668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.133841 restraints weight = 5642.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.137533 restraints weight = 3416.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.139980 restraints weight = 2476.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.141472 restraints weight = 1992.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.142606 restraints weight = 1729.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4289  Z= 0.123
  Angle     :  0.592  11.919   5839  Z= 0.290
  Chirality :  0.044   0.170    648
  Planarity :  0.004   0.040    743
  Dihedral  :  4.391  26.542    611
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.17 %
    Favored  : 84.57 %
  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:  0.04 (0.39), residues: 506
  helix:  0.79 (0.61), residues: 73
  sheet:  0.19 (0.39), residues: 164
  loop : -0.20 (0.42), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 267 
 TYR   0.025   0.002   TYR H  99 
 PHE   0.008   0.001   PHE A 663 
 TRP   0.010   0.001   TRP A  84 
 HIS   0.002   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4284)
  covalent geometry    : angle       0.59035 ( 5827)
  SS BOND              : bond        0.00342 (    3)
  SS BOND              : angle       0.50464 (    6)
  hydrogen bonds       : bond        0.03098 (  141)
  hydrogen bonds       : angle       4.48696 (  348)
  link_BETA1-4         : bond        0.01117 (    1)
  link_BETA1-4         : angle       2.02168 (    3)
  link_NAG-ASN         : bond        0.00583 (    1)
  link_NAG-ASN         : angle       1.10367 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7281 (mttt) cc_final: 0.5930 (mptt)
REVERT: H   91 THR cc_start: 0.8803 (m) cc_final: 0.8341 (p)
  outliers start: 15
  outliers final: 14
  residues processed: 75
  average time/residue: 0.0674
  time to fit residues: 6.5287
Evaluate side-chains
  77 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   93 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0670
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
H  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.159645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.132850 restraints weight = 5620.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.136543 restraints weight = 3400.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.138873 restraints weight = 2457.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.140572 restraints weight = 1989.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.141571 restraints weight = 1711.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4289  Z= 0.135
  Angle     :  0.613  11.655   5839  Z= 0.301
  Chirality :  0.044   0.158    648
  Planarity :  0.004   0.042    743
  Dihedral  :  4.390  24.549    611
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.39 %
    Favored  : 84.57 %
  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: -0.05 (0.39), residues: 506
  helix:  0.61 (0.60), residues: 75
  sheet:  0.15 (0.39), residues: 164
  loop : -0.24 (0.42), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 267 
 TYR   0.025   0.002   TYR H  99 
 PHE   0.013   0.001   PHE L  87 
 TRP   0.009   0.001   TRP A  84 
 HIS   0.002   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4284)
  covalent geometry    : angle       0.61094 ( 5827)
  SS BOND              : bond        0.00326 (    3)
  SS BOND              : angle       0.58782 (    6)
  hydrogen bonds       : bond        0.03136 (  141)
  hydrogen bonds       : angle       4.50761 (  348)
  link_BETA1-4         : bond        0.01272 (    1)
  link_BETA1-4         : angle       2.07956 (    3)
  link_NAG-ASN         : bond        0.00615 (    1)
  link_NAG-ASN         : angle       1.12922 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7264 (mttt) cc_final: 0.5876 (mptt)
REVERT: H   87 THR cc_start: 0.7872 (m) cc_final: 0.7342 (p)
REVERT: H   91 THR cc_start: 0.8833 (m) cc_final: 0.8382 (p)
  outliers start: 14
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0599
  time to fit residues: 5.8547
Evaluate side-chains
  79 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   93 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3776 r_free = 0.3776 target = 0.160356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.133383 restraints weight = 5555.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.137047 restraints weight = 3413.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.139489 restraints weight = 2490.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141131 restraints weight = 2012.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.142026 restraints weight = 1740.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4289  Z= 0.124
  Angle     :  0.602  11.466   5839  Z= 0.296
  Chirality :  0.043   0.159    648
  Planarity :  0.004   0.041    743
  Dihedral  :  4.317  20.369    611
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.26 %
    Favored  : 83.91 %
  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: -0.07 (0.39), residues: 506
  helix:  0.66 (0.60), residues: 75
  sheet:  0.14 (0.39), residues: 164
  loop : -0.28 (0.42), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 267 
 TYR   0.024   0.001   TYR H  99 
 PHE   0.009   0.001   PHE A  65 
 TRP   0.010   0.001   TRP A  84 
 HIS   0.001   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4284)
  covalent geometry    : angle       0.59991 ( 5827)
  SS BOND              : bond        0.00343 (    3)
  SS BOND              : angle       0.54350 (    6)
  hydrogen bonds       : bond        0.03030 (  141)
  hydrogen bonds       : angle       4.48818 (  348)
  link_BETA1-4         : bond        0.01155 (    1)
  link_BETA1-4         : angle       2.07277 (    3)
  link_NAG-ASN         : bond        0.00510 (    1)
  link_NAG-ASN         : angle       1.09840 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.123 
Fit side-chains
REVERT: H   91 THR cc_start: 0.8841 (m) cc_final: 0.8394 (p)
  outliers start: 13
  outliers final: 13
  residues processed: 72
  average time/residue: 0.0637
  time to fit residues: 5.9533
Evaluate side-chains
  77 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   93 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0570
   chunk 16 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 32 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
H  55 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.161229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.134153 restraints weight = 5637.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.137919 restraints weight = 3429.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.140398 restraints weight = 2485.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.141904 restraints weight = 1999.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.143110 restraints weight = 1737.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4289  Z= 0.116
  Angle     :  0.599  11.484   5839  Z= 0.292
  Chirality :  0.043   0.155    648
  Planarity :  0.004   0.040    743
  Dihedral  :  4.261  21.665    611
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.48 %
    Favored  : 83.48 %
  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:  0.00 (0.39), residues: 506
  helix:  0.68 (0.60), residues: 75
  sheet:  0.35 (0.40), residues: 157
  loop : -0.33 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 267 
 TYR   0.023   0.001   TYR H  99 
 PHE   0.013   0.001   PHE L  87 
 TRP   0.011   0.001   TRP A  84 
 HIS   0.001   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4284)
  covalent geometry    : angle       0.59747 ( 5827)
  SS BOND              : bond        0.00332 (    3)
  SS BOND              : angle       0.58448 (    6)
  hydrogen bonds       : bond        0.02959 (  141)
  hydrogen bonds       : angle       4.46497 (  348)
  link_BETA1-4         : bond        0.01143 (    1)
  link_BETA1-4         : angle       2.07782 (    3)
  link_NAG-ASN         : bond        0.00419 (    1)
  link_NAG-ASN         : angle       1.05043 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.095 
Fit side-chains
REVERT: H   91 THR cc_start: 0.8799 (m) cc_final: 0.8361 (p)
  outliers start: 14
  outliers final: 14
  residues processed: 74
  average time/residue: 0.0516
  time to fit residues: 5.0566
Evaluate side-chains
  78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   93 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
H   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.159428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.132788 restraints weight = 5515.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.136432 restraints weight = 3377.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.138843 restraints weight = 2452.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.140270 restraints weight = 1978.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.141468 restraints weight = 1718.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4289  Z= 0.138
  Angle     :  0.619  11.253   5839  Z= 0.304
  Chirality :  0.044   0.150    648
  Planarity :  0.004   0.042    743
  Dihedral  :  4.392  23.777    611
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.83 %
    Favored  : 83.91 %
  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: -0.06 (0.39), residues: 506
  helix:  0.59 (0.60), residues: 75
  sheet:  0.30 (0.40), residues: 157
  loop : -0.35 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 267 
 TYR   0.025   0.002   TYR H  99 
 PHE   0.010   0.001   PHE A  65 
 TRP   0.008   0.001   TRP A  84 
 HIS   0.002   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4284)
  covalent geometry    : angle       0.61717 ( 5827)
  SS BOND              : bond        0.00337 (    3)
  SS BOND              : angle       0.64505 (    6)
  hydrogen bonds       : bond        0.03127 (  141)
  hydrogen bonds       : angle       4.51572 (  348)
  link_BETA1-4         : bond        0.01203 (    1)
  link_BETA1-4         : angle       2.04071 (    3)
  link_NAG-ASN         : bond        0.00617 (    1)
  link_NAG-ASN         : angle       1.19164 (    3)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  184 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7289 (ttp-170)
REVERT: H   91 THR cc_start: 0.8845 (m) cc_final: 0.8390 (p)
  outliers start: 15
  outliers final: 15
  residues processed: 70
  average time/residue: 0.0583
  time to fit residues: 5.4486
Evaluate side-chains
  74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   93 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3757 r_free = 0.3757 target = 0.158539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.131420 restraints weight = 5609.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.135084 restraints weight = 3432.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.137513 restraints weight = 2510.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.139081 restraints weight = 2032.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.140221 restraints weight = 1758.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4289  Z= 0.157
  Angle     :  0.634  11.174   5839  Z= 0.312
  Chirality :  0.045   0.152    648
  Planarity :  0.004   0.042    743
  Dihedral  :  4.567  24.950    611
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.48 %
    Favored  : 83.26 %
  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: -0.17 (0.39), residues: 506
  helix:  0.45 (0.59), residues: 75
  sheet:  0.10 (0.39), residues: 162
  loop : -0.32 (0.42), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 267 
 TYR   0.025   0.002   TYR H  99 
 PHE   0.015   0.002   PHE L  87 
 TRP   0.008   0.001   TRP A 178 
 HIS   0.004   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4284)
  covalent geometry    : angle       0.63159 ( 5827)
  SS BOND              : bond        0.00342 (    3)
  SS BOND              : angle       0.67678 (    6)
  hydrogen bonds       : bond        0.03237 (  141)
  hydrogen bonds       : angle       4.58003 (  348)
  link_BETA1-4         : bond        0.01147 (    1)
  link_BETA1-4         : angle       2.06583 (    3)
  link_NAG-ASN         : bond        0.00767 (    1)
  link_NAG-ASN         : angle       1.23733 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 911.03 seconds
wall clock time: 16 minutes 18.71 seconds (978.71 seconds total)