Starting phenix.real_space_refine
on Wed Jul 23 20:28:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lkh_23408/07_2025/7lkh_23408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lkh_23408/07_2025/7lkh_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2025/7lkh_23408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2025/7lkh_23408.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2025/7lkh_23408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2025/7lkh_23408.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.44, per 1000 atoms: 1.06
  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: 1.13
  Conformation dependent library (CDL) restraints added in 903.1 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: 0.83
  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: 1.32

  Time building geometry restraints manager: 1.37 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:             61.550
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     18.900
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   84.350
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.014   0.002   TRP H  47 
 HIS   0.004   0.001   HIS A 273 
 PHE   0.037   0.003   PHE A  65 
 TYR   0.031   0.003   TYR A  64 
 ARG   0.013   0.001   ARG A 230 

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

*********************** 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  : 0.518 
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: 0.2233
  time to fit residues: 21.9952
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  : 0.491 
-------------------------------------------------------------------------------
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 42 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.158303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.131502 restraints weight = 5550.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.135274 restraints weight = 3369.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.137712 restraints weight = 2437.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4289  Z= 0.167
  Angle     :  0.716  14.069   5839  Z= 0.352
  Chirality :  0.048   0.164    648
  Planarity :  0.006   0.070    743
  Dihedral  :  6.282  59.155    613
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  6.09 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.37), residues: 506
  helix:  0.25 (0.60), residues: 72
  sheet: -0.06 (0.38), residues: 165
  loop : -0.60 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 167 
 PHE   0.011   0.002   PHE L  98 
 TYR   0.036   0.002   TYR H  99 
 ARG   0.005   0.001   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00874 (    1)
  link_NAG-ASN         : angle       1.47979 (    3)
  link_BETA1-4         : bond        0.00314 (    1)
  link_BETA1-4         : angle       3.30731 (    3)
  hydrogen bonds       : bond        0.03610 (  141)
  hydrogen bonds       : angle       5.12030 (  348)
  SS BOND              : bond        0.00317 (    3)
  SS BOND              : angle       0.56064 (    6)
  covalent geometry    : bond        0.00396 ( 4284)
  covalent geometry    : angle       0.71164 ( 5827)

*********************** 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
  71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.598 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7335 (mttt) cc_final: 0.6534 (mppt)
REVERT: A  244 ASP cc_start: 0.7169 (t70) cc_final: 0.6790 (t70)
  outliers start: 10
  outliers final: 5
  residues processed: 69
  average time/residue: 0.1522
  time to fit residues: 13.8991
Evaluate side-chains
  54 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.159569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.132510 restraints weight = 5574.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.136262 restraints weight = 3389.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.138735 restraints weight = 2462.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1943

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= 0.127
  Angle     :  0.643  13.261   5839  Z= 0.313
  Chirality :  0.045   0.157    648
  Planarity :  0.005   0.052    743
  Dihedral  :  5.466  53.269    611
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.91 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.38), residues: 506
  helix:  0.56 (0.61), residues: 72
  sheet:  0.11 (0.39), residues: 167
  loop : -0.41 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 198 
 PHE   0.008   0.001   PHE L  98 
 TYR   0.029   0.002   TYR H  99 
 ARG   0.004   0.000   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00393 (    1)
  link_NAG-ASN         : angle       0.95770 (    3)
  link_BETA1-4         : bond        0.00994 (    1)
  link_BETA1-4         : angle       2.82404 (    3)
  hydrogen bonds       : bond        0.03202 (  141)
  hydrogen bonds       : angle       4.80757 (  348)
  SS BOND              : bond        0.00266 (    3)
  SS BOND              : angle       0.89962 (    6)
  covalent geometry    : bond        0.00294 ( 4284)
  covalent geometry    : angle       0.63928 ( 5827)

*********************** 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
  75 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7400 (mttt) cc_final: 0.6662 (mppt)
REVERT: H   87 THR cc_start: 0.7817 (m) cc_final: 0.7343 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 74
  average time/residue: 0.2125
  time to fit residues: 20.4395
Evaluate side-chains
  59 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.156773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.129741 restraints weight = 5572.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.133433 restraints weight = 3361.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.135862 restraints weight = 2438.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4289  Z= 0.150
  Angle     :  0.656  12.007   5839  Z= 0.320
  Chirality :  0.045   0.155    648
  Planarity :  0.005   0.060    743
  Dihedral  :  5.211  47.311    611
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 10.00 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.38), residues: 506
  helix:  0.62 (0.61), residues: 72
  sheet:  0.05 (0.39), residues: 166
  loop : -0.28 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 198 
 PHE   0.010   0.001   PHE A 663 
 TYR   0.028   0.002   TYR H  99 
 ARG   0.003   0.000   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00665 (    1)
  link_NAG-ASN         : angle       1.16364 (    3)
  link_BETA1-4         : bond        0.01059 (    1)
  link_BETA1-4         : angle       2.59946 (    3)
  hydrogen bonds       : bond        0.03296 (  141)
  hydrogen bonds       : angle       4.79265 (  348)
  SS BOND              : bond        0.00481 (    3)
  SS BOND              : angle       0.67422 (    6)
  covalent geometry    : bond        0.00354 ( 4284)
  covalent geometry    : angle       0.65299 ( 5827)

*********************** 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
  77 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7318 (mttt) cc_final: 0.6293 (mppt)
REVERT: H   87 THR cc_start: 0.7838 (m) cc_final: 0.7274 (p)
REVERT: L   28 ASP cc_start: 0.8095 (p0) cc_final: 0.7836 (p0)
REVERT: L   34 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8523 (m-40)
  outliers start: 16
  outliers final: 12
  residues processed: 72
  average time/residue: 0.1489
  time to fit residues: 13.9107
Evaluate side-chains
  67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
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 A residue  272 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   34 ASN
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   52 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.140946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.113442 restraints weight = 5842.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.116614 restraints weight = 3698.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.118738 restraints weight = 2743.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4289  Z= 0.174
  Angle     :  0.667  11.905   5839  Z= 0.326
  Chirality :  0.046   0.163    648
  Planarity :  0.005   0.049    743
  Dihedral  :  5.104  42.263    611
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 11.09 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.38), residues: 506
  helix:  0.47 (0.60), residues: 73
  sheet:  0.01 (0.39), residues: 165
  loop : -0.35 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  84 
 HIS   0.010   0.001   HIS A 198 
 PHE   0.010   0.001   PHE A 663 
 TYR   0.028   0.002   TYR H  99 
 ARG   0.003   0.000   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00871 (    1)
  link_NAG-ASN         : angle       1.33088 (    3)
  link_BETA1-4         : bond        0.01044 (    1)
  link_BETA1-4         : angle       2.38487 (    3)
  hydrogen bonds       : bond        0.03468 (  141)
  hydrogen bonds       : angle       4.81509 (  348)
  SS BOND              : bond        0.00348 (    3)
  SS BOND              : angle       0.63695 (    6)
  covalent geometry    : bond        0.00416 ( 4284)
  covalent geometry    : angle       0.66448 ( 5827)

*********************** 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
  76 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.463 
Fit side-chains
REVERT: L   28 ASP cc_start: 0.8052 (p0) cc_final: 0.7826 (p0)
  outliers start: 18
  outliers final: 15
  residues processed: 71
  average time/residue: 0.1528
  time to fit residues: 14.1274
Evaluate side-chains
  70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
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  157 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  272 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   75 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    0.0050
   chunk 9 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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 = 0.158601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.131505 restraints weight = 5530.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.135202 restraints weight = 3351.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.137656 restraints weight = 2430.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4289  Z= 0.137
  Angle     :  0.634  11.791   5839  Z= 0.309
  Chirality :  0.044   0.168    648
  Planarity :  0.005   0.047    743
  Dihedral  :  4.849  37.280    611
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.83 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.39), residues: 506
  helix:  0.49 (0.60), residues: 73
  sheet:  0.02 (0.39), residues: 165
  loop : -0.35 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  84 
 HIS   0.012   0.001   HIS A 198 
 PHE   0.008   0.001   PHE A 663 
 TYR   0.027   0.002   TYR H  99 
 ARG   0.006   0.000   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00618 (    1)
  link_NAG-ASN         : angle       1.12402 (    3)
  link_BETA1-4         : bond        0.01102 (    1)
  link_BETA1-4         : angle       2.27741 (    3)
  hydrogen bonds       : bond        0.03228 (  141)
  hydrogen bonds       : angle       4.73418 (  348)
  SS BOND              : bond        0.00307 (    3)
  SS BOND              : angle       0.58624 (    6)
  covalent geometry    : bond        0.00321 ( 4284)
  covalent geometry    : angle       0.63204 ( 5827)

*********************** 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
  69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.497 
Fit side-chains
REVERT: L   28 ASP cc_start: 0.8028 (p0) cc_final: 0.7819 (p0)
  outliers start: 14
  outliers final: 12
  residues processed: 63
  average time/residue: 0.1558
  time to fit residues: 12.9893
Evaluate side-chains
  72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  157 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 H residue   18 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
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   75 ILE
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 31 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0170
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0970
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.4616

-------------------------------------------------------------------------------
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 = 0.3765 r_free = 0.3765 target = 0.159066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.131985 restraints weight = 5507.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.135669 restraints weight = 3351.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.138101 restraints weight = 2445.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2799

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= 0.113
  Angle     :  0.599  11.656   5839  Z= 0.291
  Chirality :  0.043   0.154    648
  Planarity :  0.004   0.043    743
  Dihedral  :  4.370  25.665    611
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.26 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.39), residues: 506
  helix:  0.55 (0.61), residues: 73
  sheet:  0.12 (0.39), residues: 164
  loop : -0.34 (0.42), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  84 
 HIS   0.009   0.001   HIS A 198 
 PHE   0.007   0.001   PHE A 663 
 TYR   0.024   0.001   TYR H  99 
 ARG   0.006   0.000   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00402 (    1)
  link_NAG-ASN         : angle       1.05565 (    3)
  link_BETA1-4         : bond        0.01316 (    1)
  link_BETA1-4         : angle       2.17789 (    3)
  hydrogen bonds       : bond        0.02997 (  141)
  hydrogen bonds       : angle       4.57825 (  348)
  SS BOND              : bond        0.00333 (    3)
  SS BOND              : angle       0.53567 (    6)
  covalent geometry    : bond        0.00258 ( 4284)
  covalent geometry    : angle       0.59660 ( 5827)

*********************** 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
  77 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.498 
Fit side-chains
  outliers start: 12
  outliers final: 12
  residues processed: 73
  average time/residue: 0.1496
  time to fit residues: 14.1852
Evaluate side-chains
  70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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 A residue  264 CYS
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 L residue    8 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   75 ILE
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 33 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 30 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3748 r_free = 0.3748 target = 0.157533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.130176 restraints weight = 5541.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.133810 restraints weight = 3403.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.136154 restraints weight = 2485.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2880

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= 0.136
  Angle     :  0.634  11.513   5839  Z= 0.309
  Chirality :  0.044   0.165    648
  Planarity :  0.004   0.044    743
  Dihedral  :  4.386  22.052    611
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.61 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.39), residues: 506
  helix:  0.46 (0.60), residues: 73
  sheet:  0.10 (0.39), residues: 164
  loop : -0.36 (0.42), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  84 
 HIS   0.010   0.001   HIS A 198 
 PHE   0.014   0.001   PHE L  87 
 TYR   0.025   0.002   TYR H  99 
 ARG   0.007   0.000   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00642 (    1)
  link_NAG-ASN         : angle       1.17348 (    3)
  link_BETA1-4         : bond        0.01137 (    1)
  link_BETA1-4         : angle       2.09185 (    3)
  hydrogen bonds       : bond        0.03207 (  141)
  hydrogen bonds       : angle       4.63221 (  348)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       0.61099 (    6)
  covalent geometry    : bond        0.00319 ( 4284)
  covalent geometry    : angle       0.63186 ( 5827)

*********************** 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
  76 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.555 
Fit side-chains
  outliers start: 14
  outliers final: 13
  residues processed: 72
  average time/residue: 0.1431
  time to fit residues: 13.6236
Evaluate side-chains
  72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  146 VAL
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  641 VAL
Chi-restraints excluded: chain H residue   18 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
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   75 ILE
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 19 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0980
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   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 = 0.3756 r_free = 0.3756 target = 0.158365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.131125 restraints weight = 5539.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.134781 restraints weight = 3389.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.137221 restraints weight = 2469.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2950

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= 0.126
  Angle     :  0.617  11.530   5839  Z= 0.300
  Chirality :  0.044   0.157    648
  Planarity :  0.004   0.043    743
  Dihedral  :  4.324  19.409    611
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.48 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.39), residues: 506
  helix:  0.49 (0.61), residues: 73
  sheet:  0.32 (0.40), residues: 157
  loop : -0.43 (0.41), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  84 
 HIS   0.010   0.001   HIS A 198 
 PHE   0.007   0.001   PHE A 663 
 TYR   0.023   0.001   TYR H  99 
 ARG   0.007   0.000   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00507 (    1)
  link_NAG-ASN         : angle       1.06573 (    3)
  link_BETA1-4         : bond        0.01212 (    1)
  link_BETA1-4         : angle       2.12722 (    3)
  hydrogen bonds       : bond        0.03122 (  141)
  hydrogen bonds       : angle       4.55118 (  348)
  SS BOND              : bond        0.00365 (    3)
  SS BOND              : angle       0.59879 (    6)
  covalent geometry    : bond        0.00293 ( 4284)
  covalent geometry    : angle       0.61521 ( 5827)

*********************** 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
  72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.493 
Fit side-chains
  outliers start: 12
  outliers final: 11
  residues processed: 68
  average time/residue: 0.1477
  time to fit residues: 13.1685
Evaluate side-chains
  68 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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 A residue  264 CYS
Chi-restraints excluded: chain A residue  641 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
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   75 ILE
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 47 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 11 optimal weight:    0.2980
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3783 r_free = 0.3783 target = 0.161065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.133935 restraints weight = 5520.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.137574 restraints weight = 3384.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.139971 restraints weight = 2479.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3029

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= 0.120
  Angle     :  0.613  11.626   5839  Z= 0.299
  Chirality :  0.043   0.155    648
  Planarity :  0.004   0.043    743
  Dihedral  :  4.273  19.548    611
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.04 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.39), residues: 506
  helix:  0.38 (0.60), residues: 75
  sheet:  0.34 (0.40), residues: 157
  loop : -0.42 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  84 
 HIS   0.009   0.001   HIS A 198 
 PHE   0.012   0.001   PHE L  87 
 TYR   0.023   0.001   TYR H  99 
 ARG   0.007   0.000   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00446 (    1)
  link_NAG-ASN         : angle       1.04261 (    3)
  link_BETA1-4         : bond        0.01185 (    1)
  link_BETA1-4         : angle       2.12930 (    3)
  hydrogen bonds       : bond        0.03049 (  141)
  hydrogen bonds       : angle       4.49908 (  348)
  SS BOND              : bond        0.00335 (    3)
  SS BOND              : angle       0.61917 (    6)
  covalent geometry    : bond        0.00276 ( 4284)
  covalent geometry    : angle       0.61084 ( 5827)

********************** 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
  72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.540 
Fit side-chains
REVERT: H   99 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.6181 (p90)
  outliers start: 12
  outliers final: 11
  residues processed: 69
  average time/residue: 0.1490
  time to fit residues: 13.5538
Evaluate side-chains
  70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  146 VAL
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  641 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
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   75 ILE
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:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0040
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0570
   chunk 41 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.3910

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.160684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.133464 restraints weight = 5495.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.137096 restraints weight = 3378.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.139481 restraints weight = 2478.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.3110

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= 0.108
  Angle     :  0.592  11.686   5839  Z= 0.288
  Chirality :  0.043   0.148    648
  Planarity :  0.004   0.042    743
  Dihedral  :  4.223  25.146    611
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.39), residues: 506
  helix:  0.45 (0.61), residues: 75
  sheet:  0.43 (0.41), residues: 157
  loop : -0.39 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  84 
 HIS   0.007   0.001   HIS A 198 
 PHE   0.007   0.001   PHE L  98 
 TYR   0.021   0.001   TYR H  99 
 ARG   0.007   0.000   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00311 (    1)
  link_NAG-ASN         : angle       1.02340 (    3)
  link_BETA1-4         : bond        0.01172 (    1)
  link_BETA1-4         : angle       2.11508 (    3)
  hydrogen bonds       : bond        0.02911 (  141)
  hydrogen bonds       : angle       4.38746 (  348)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       0.59974 (    6)
  covalent geometry    : bond        0.00246 ( 4284)
  covalent geometry    : angle       0.58998 ( 5827)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2030.86 seconds
wall clock time: 36 minutes 48.80 seconds (2208.80 seconds total)