Starting phenix.real_space_refine
on Tue Mar  3 12:37:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sj0_25149/03_2026/7sj0_25149.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sj0_25149/03_2026/7sj0_25149.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sj0_25149/03_2026/7sj0_25149.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sj0_25149/03_2026/7sj0_25149.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sj0_25149/03_2026/7sj0_25149.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sj0_25149/03_2026/7sj0_25149.map"
  }
  resolution = 3.36
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 812 atoms to isotropic.
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      14      5.16       5
     C    2279      2.51       5
     N     593      2.21       5
     O     704      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3590
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1806
          Classifications: {'peptide': 224}
          Link IDs: {'PTRANS': 10, 'TRANS': 213}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 930
          Classifications: {'peptide': 120}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 784
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 7, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.02, per 1000 atoms: 0.28
  Number of scatterers: 3590
  At special positions: 0
  Unit cell: (99, 78.1, 94.6, 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      14     16.00
     O     704      8.00
     N     593      7.00
     C    2279      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " 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
    NAG-ASN
      " NAG A1301 " - " ASN A 122 "
      " NAG A1302 " - " ASN A 165 "
      " NAG A1303 " - " ASN A  17 "
      " NAG A1304 " - " ASN A  61 "
      " NAG A1305 " - " ASN A 149 "
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 130.3 milliseconds
  

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  824

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 9 sheets defined
      2.0% alpha, 36.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 156 through 159
    Processing helix  chain 'B' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29
      removed outlier: 4.312A  pdb=" N   ALA A  27 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TRP A  64 " --> pdb=" O   ALA A  27 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL A 267 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TYR A 265 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA A  93 " --> pdb=" O   TYR A 266 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A  90 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER A  94 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   THR A 208 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLU A 191 " --> pdb=" O   LYS A 206 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LYS A 206 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79
      removed outlier: 4.045A  pdb=" N   ARG A  78 " --> pdb=" O   HIS A  69 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   HIS A  69 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL A 267 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TYR A 265 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA A  93 " --> pdb=" O   TYR A 266 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A  90 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER A  94 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LYS A 195 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS A 202 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.702A  pdb=" N   CYS A 131 " --> pdb=" O   SER A 116 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL A 126 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   SER A 172 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 155
      removed outlier: 4.000A  pdb=" N   SER A 151 " --> pdb=" O   HIS A 146 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY A 142 " --> pdb=" O   SER A 155 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.735A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 3.846A  pdb=" N   THR B 119 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL B 118 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA B  92 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLY B  99 " --> pdb=" O   SER B  33 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER B  33 " --> pdb=" O   GLY B  99 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   MET B  34 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   GLY B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   TRP B  36 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA B  40 " --> pdb=" O   GLY B  44 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLY B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 12
    Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23
      removed outlier: 3.525A  pdb=" N   VAL L  18 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE L  76 " --> pdb=" O   VAL L  18 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 46 through 50
      removed outlier: 3.640A  pdb=" N   GLN L  38 " --> pdb=" O   LYS L  46 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER L  35 " --> pdb=" O   GLY L  90 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLY L  90 " --> pdb=" O   SER L  35 " (cutoff:3.500A)

    93 hydrogen bonds defined for protein.
    228 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: 0.45

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1130
        1.34 -     1.46: 942
        1.46 -     1.58: 1584
        1.58 -     1.70: 0
        1.70 -     1.82: 20
  Bond restraints: 3676
  Sorted by residual:
  bond pdb=" C1  NAG A1305 "
       pdb=" O5  NAG A1305 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.14e+00
  bond pdb=" C1  NAG A1304 "
       pdb=" O5  NAG A1304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.94e+00
  bond pdb=" C1  NAG A1303 "
       pdb=" O5  NAG A1303 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.76e+00
  bond pdb=" C1  NAG A1302 "
       pdb=" O5  NAG A1302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.56e+00
  ... (remaining 3671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 4795
        1.51 -     3.02: 173
        3.02 -     4.53: 22
        4.53 -     6.04: 4
        6.04 -     7.54: 2
  Bond angle restraints: 4996
  Sorted by residual:
  angle pdb=" CA  THR A  33 "
        pdb=" CB  THR A  33 "
        pdb=" CG2 THR A  33 "
      ideal   model   delta    sigma   weight residual
     110.50  114.45   -3.95 1.70e+00 3.46e-01 5.39e+00
  angle pdb=" CA  CYS A 131 "
        pdb=" CB  CYS A 131 "
        pdb=" SG  CYS A 131 "
      ideal   model   delta    sigma   weight residual
     114.40  119.53   -5.13 2.30e+00 1.89e-01 4.98e+00
  angle pdb=" CA  LEU L  96 "
        pdb=" CB  LEU L  96 "
        pdb=" CG  LEU L  96 "
      ideal   model   delta    sigma   weight residual
     116.30  123.84   -7.54 3.50e+00 8.16e-02 4.65e+00
  angle pdb=" CB  MET B  34 "
        pdb=" CG  MET B  34 "
        pdb=" SD  MET B  34 "
      ideal   model   delta    sigma   weight residual
     112.70  118.84   -6.14 3.00e+00 1.11e-01 4.20e+00
  angle pdb=" C   PHE A  32 "
        pdb=" N   THR A  33 "
        pdb=" CA  THR A  33 "
      ideal   model   delta    sigma   weight residual
     122.68  125.62   -2.94 1.47e+00 4.63e-01 4.01e+00
  ... (remaining 4991 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 2034
       17.30 -    34.60: 135
       34.60 -    51.90: 33
       51.90 -    69.20: 8
       69.20 -    86.49: 3
  Dihedral angle restraints: 2213
    sinusoidal: 922
      harmonic: 1291
  Sorted by residual:
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -135.37   49.37     1      1.00e+01 1.00e-02 3.35e+01
  dihedral pdb=" CA  ASN A  99 "
           pdb=" C   ASN A  99 "
           pdb=" N   ILE A 100 "
           pdb=" CA  ILE A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.53   23.47     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  THR A 167 "
           pdb=" C   THR A 167 "
           pdb=" N   PHE A 168 "
           pdb=" CA  PHE A 168 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.25  -22.75     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 2210 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 503
       0.082 -    0.164: 60
       0.164 -    0.246: 0
       0.246 -    0.328: 1
       0.328 -    0.410: 1
  Chirality restraints: 565
  Sorted by residual:
  chirality pdb=" C1  NAG A1304 "
            pdb=" ND2 ASN A  61 "
            pdb=" C2  NAG A1304 "
            pdb=" O5  NAG A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.99   -0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" C1  NAG A1302 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A1302 "
            pdb=" O5  NAG A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  ILE L  49 "
            pdb=" N   ILE L  49 "
            pdb=" C   ILE L  49 "
            pdb=" CB  ILE L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.27e-01
  ... (remaining 562 not shown)

  Planarity restraints: 637
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG L  55 "    0.020 5.00e-02 4.00e+02   3.04e-02 1.48e+00
        pdb=" N   PRO L  56 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO L  56 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO L  56 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  99 "   -0.006 2.00e-02 2.50e+03   1.21e-02 1.46e+00
        pdb=" C   ASN A  99 "    0.021 2.00e-02 2.50e+03
        pdb=" O   ASN A  99 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ILE A 100 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  61 "   -0.010 2.00e-02 2.50e+03   9.87e-03 1.22e+00
        pdb=" CG  ASN A  61 "    0.010 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  61 "   -0.002 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  61 "    0.013 2.00e-02 2.50e+03
        pdb=" C1  NAG A1304 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 634 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 512
        2.76 -     3.30: 3344
        3.30 -     3.83: 4986
        3.83 -     4.37: 5454
        4.37 -     4.90: 10160
  Nonbonded interactions: 24456
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  68 "
            pdb=" OG  SER L  71 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   GLY L  30 "
            pdb=" NZ  LYS L  67 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OG1 THR A 109 "
            pdb=" OD1 ASP A 111 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" NZ  LYS A 129 "
            pdb=" O   PHE A 168 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" OG1 THR A 124 "
            pdb=" O7  NAG A1301 "
     model   vdw
     2.337 3.040
  ... (remaining 24451 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.350
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3685  Z= 0.150
  Angle     :  0.695  11.271   5019  Z= 0.340
  Chirality :  0.052   0.410    565
  Planarity :  0.004   0.030    632
  Dihedral  : 12.810  86.494   1377
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.98 (0.38), residues: 438
  helix:  None (None), residues: 0
  sheet: -0.01 (0.42), residues: 141
  loop : -2.13 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 190 
 TYR   0.010   0.001   TYR B  27 
 PHE   0.012   0.001   PHE A 238 
 TRP   0.007   0.001   TRP B 108 
 HIS   0.001   0.000   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3676)
  covalent geometry    : angle       0.65582 ( 4996)
  SS BOND              : bond        0.00359 (    4)
  SS BOND              : angle       1.09922 (    8)
  hydrogen bonds       : bond        0.31461 (   83)
  hydrogen bonds       : angle      10.57815 (  228)
  link_NAG-ASN         : bond        0.01028 (    5)
  link_NAG-ASN         : angle       4.20517 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   69 HIS cc_start: 0.7608 (t-90) cc_final: 0.7232 (t-90)
REVERT: A  144 TYR cc_start: 0.8296 (p90) cc_final: 0.8091 (p90)
REVERT: A  202 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8367 (mtpt)
REVERT: B   64 PHE cc_start: 0.8333 (m-10) cc_final: 0.8057 (m-10)
REVERT: B  107 ASN cc_start: 0.7869 (p0) cc_final: 0.7609 (p0)
REVERT: L   76 ILE cc_start: 0.8006 (tp) cc_final: 0.7749 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0740
  time to fit residues: 9.4354
Evaluate side-chains
  94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0170
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.2218

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A  99 ASN
B   1 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.106013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.088947 restraints weight = 8899.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 4.25
r_work: 0.3258 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3685  Z= 0.124
  Angle     :  0.703  13.212   5019  Z= 0.348
  Chirality :  0.052   0.455    565
  Planarity :  0.004   0.031    632
  Dihedral  :  7.363  59.775    587
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.31 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.63 (0.38), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.51 (0.42), residues: 144
  loop : -2.07 (0.33), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  34 
 TYR   0.011   0.001   TYR A 145 
 PHE   0.011   0.001   PHE B 102 
 TRP   0.008   0.002   TRP L  92 
 HIS   0.001   0.000   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3676)
  covalent geometry    : angle       0.65590 ( 4996)
  SS BOND              : bond        0.00578 (    4)
  SS BOND              : angle       1.13280 (    8)
  hydrogen bonds       : bond        0.04329 (   83)
  hydrogen bonds       : angle       6.93773 (  228)
  link_NAG-ASN         : bond        0.01157 (    5)
  link_NAG-ASN         : angle       4.64693 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  177 MET cc_start: 0.7575 (ppp) cc_final: 0.7369 (ppp)
REVERT: A  187 LYS cc_start: 0.7465 (mmtt) cc_final: 0.7225 (mmmt)
REVERT: A  202 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8551 (mtpt)
REVERT: A  218 GLN cc_start: 0.8529 (pp30) cc_final: 0.8286 (tm-30)
REVERT: B  107 ASN cc_start: 0.8417 (p0) cc_final: 0.8099 (p0)
REVERT: L   32 ASN cc_start: 0.7835 (m-40) cc_final: 0.7595 (m-40)
REVERT: L   55 ARG cc_start: 0.7843 (ptm160) cc_final: 0.7569 (ptm160)
REVERT: L   76 ILE cc_start: 0.7993 (tp) cc_final: 0.7757 (tt)
  outliers start: 6
  outliers final: 1
  residues processed: 106
  average time/residue: 0.0762
  time to fit residues: 9.8000
Evaluate side-chains
  92 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 43 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0970
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0070
   chunk 15 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 5 optimal weight:    0.3980
   chunk 38 optimal weight:    0.0970
   chunk 17 optimal weight:    0.0570
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.1312

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
L   6 GLN
L  32 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.107835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.090619 restraints weight = 8813.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 4.21
r_work: 0.3288 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3685  Z= 0.104
  Angle     :  0.641  11.820   5019  Z= 0.318
  Chirality :  0.049   0.404    565
  Planarity :  0.005   0.066    632
  Dihedral  :  7.006  59.488    587
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.62 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.39 (0.39), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.72 (0.43), residues: 142
  loop : -1.92 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 102 
 TYR   0.008   0.001   TYR A 145 
 PHE   0.009   0.001   PHE A  92 
 TRP   0.015   0.001   TRP B 108 
 HIS   0.001   0.000   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 3676)
  covalent geometry    : angle       0.59959 ( 4996)
  SS BOND              : bond        0.00419 (    4)
  SS BOND              : angle       1.21108 (    8)
  hydrogen bonds       : bond        0.03197 (   83)
  hydrogen bonds       : angle       5.83743 (  228)
  link_NAG-ASN         : bond        0.01002 (    5)
  link_NAG-ASN         : angle       4.10231 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  147 LYS cc_start: 0.8654 (ptmt) cc_final: 0.8341 (tmtt)
REVERT: A  153 MET cc_start: 0.8617 (tmm) cc_final: 0.8416 (tmm)
REVERT: A  172 SER cc_start: 0.7517 (t) cc_final: 0.6971 (m)
REVERT: A  177 MET cc_start: 0.7666 (ppp) cc_final: 0.7409 (ppp)
REVERT: A  187 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7317 (mmmt)
REVERT: A  202 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8511 (mtpt)
REVERT: B   34 MET cc_start: 0.8579 (tpp) cc_final: 0.8192 (mmm)
REVERT: B  107 ASN cc_start: 0.8353 (p0) cc_final: 0.8012 (p0)
REVERT: L   32 ASN cc_start: 0.7647 (m110) cc_final: 0.7223 (m110)
REVERT: L   33 TYR cc_start: 0.8165 (m-80) cc_final: 0.7077 (m-80)
REVERT: L   76 ILE cc_start: 0.7834 (tp) cc_final: 0.7603 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 103
  average time/residue: 0.0768
  time to fit residues: 9.4642
Evaluate side-chains
  92 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain L residue   23 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 2 optimal weight:    0.0980
   chunk 36 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0670
   chunk 10 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0970
   overall best weight:    0.2716

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.106317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.089012 restraints weight = 8758.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 4.20
r_work: 0.3262 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3685  Z= 0.122
  Angle     :  0.645  11.643   5019  Z= 0.320
  Chirality :  0.049   0.452    565
  Planarity :  0.004   0.043    632
  Dihedral  :  6.871  59.784    587
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.22 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.15 (0.39), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.83 (0.41), residues: 155
  loop : -1.84 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  55 
 TYR   0.010   0.001   TYR B  27 
 PHE   0.011   0.001   PHE A  86 
 TRP   0.011   0.001   TRP B 108 
 HIS   0.002   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3676)
  covalent geometry    : angle       0.60519 ( 4996)
  SS BOND              : bond        0.00496 (    4)
  SS BOND              : angle       1.21387 (    8)
  hydrogen bonds       : bond        0.03563 (   83)
  hydrogen bonds       : angle       5.60724 (  228)
  link_NAG-ASN         : bond        0.00995 (    5)
  link_NAG-ASN         : angle       4.05240 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   34 ARG cc_start: 0.7744 (tpp-160) cc_final: 0.7293 (tpp-160)
REVERT: A  187 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7346 (mmmt)
REVERT: A  195 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8769 (ttpp)
REVERT: A  202 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8496 (mtpt)
REVERT: A  218 GLN cc_start: 0.8265 (pp30) cc_final: 0.7919 (pp30)
REVERT: B   81 MET cc_start: 0.8766 (ttt) cc_final: 0.8532 (ttm)
REVERT: L   32 ASN cc_start: 0.7611 (m110) cc_final: 0.7156 (m110)
REVERT: L   33 TYR cc_start: 0.8143 (m-80) cc_final: 0.6979 (m-80)
REVERT: L   54 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7893 (tppt)
REVERT: L   76 ILE cc_start: 0.7942 (tp) cc_final: 0.7690 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 96
  average time/residue: 0.0796
  time to fit residues: 9.0720
Evaluate side-chains
  94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain L residue   23 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.0040
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
A 146 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.102604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.085541 restraints weight = 8788.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 4.16
r_work: 0.3200 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3685  Z= 0.206
  Angle     :  0.731  12.374   5019  Z= 0.368
  Chirality :  0.053   0.539    565
  Planarity :  0.005   0.031    632
  Dihedral  :  7.128  59.136    587
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.74 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.26 (0.39), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.70 (0.41), residues: 155
  loop : -1.87 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  62 
 TYR   0.015   0.002   TYR B  95 
 PHE   0.018   0.002   PHE A  86 
 TRP   0.014   0.002   TRP B 108 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 3676)
  covalent geometry    : angle       0.68908 ( 4996)
  SS BOND              : bond        0.00615 (    4)
  SS BOND              : angle       1.58077 (    8)
  hydrogen bonds       : bond        0.04735 (   83)
  hydrogen bonds       : angle       5.98861 (  228)
  link_NAG-ASN         : bond        0.01137 (    5)
  link_NAG-ASN         : angle       4.38457 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  153 MET cc_start: 0.8660 (tmm) cc_final: 0.8449 (tmm)
REVERT: A  170 TYR cc_start: 0.6568 (t80) cc_final: 0.5739 (t80)
REVERT: A  195 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8896 (ttpp)
REVERT: A  202 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8578 (mtpt)
REVERT: L   32 ASN cc_start: 0.7613 (m110) cc_final: 0.7314 (m-40)
REVERT: L   33 TYR cc_start: 0.8025 (m-80) cc_final: 0.6851 (m-80)
REVERT: L   62 ARG cc_start: 0.7464 (mmt180) cc_final: 0.7154 (mmt-90)
  outliers start: 10
  outliers final: 6
  residues processed: 103
  average time/residue: 0.0763
  time to fit residues: 9.3369
Evaluate side-chains
  102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain L residue   23 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0470
   chunk 39 optimal weight:    0.3980
   chunk 13 optimal weight:    0.0020
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.3086

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.104355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.087149 restraints weight = 8892.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 4.29
r_work: 0.3223 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3685  Z= 0.137
  Angle     :  0.690  11.265   5019  Z= 0.343
  Chirality :  0.050   0.474    565
  Planarity :  0.004   0.029    632
  Dihedral  :  6.754  57.968    587
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.77 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.06 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.76 (0.39), residues: 174
  loop : -1.86 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  62 
 TYR   0.010   0.001   TYR B  27 
 PHE   0.011   0.001   PHE A  86 
 TRP   0.008   0.001   TRP A 104 
 HIS   0.002   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3676)
  covalent geometry    : angle       0.65258 ( 4996)
  SS BOND              : bond        0.00778 (    4)
  SS BOND              : angle       1.40756 (    8)
  hydrogen bonds       : bond        0.03759 (   83)
  hydrogen bonds       : angle       5.73034 (  228)
  link_NAG-ASN         : bond        0.01004 (    5)
  link_NAG-ASN         : angle       4.02976 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8668 (tmm) cc_final: 0.8418 (tmm)
REVERT: A  187 LYS cc_start: 0.7380 (mmmt) cc_final: 0.7162 (mmmt)
REVERT: A  195 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8829 (ttpp)
REVERT: A  202 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8548 (mtpt)
REVERT: A  218 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7759 (pp30)
REVERT: B   81 MET cc_start: 0.8719 (ttm) cc_final: 0.8337 (ttm)
REVERT: L   32 ASN cc_start: 0.7588 (m110) cc_final: 0.7128 (m110)
REVERT: L   33 TYR cc_start: 0.8017 (m-80) cc_final: 0.6937 (m-80)
REVERT: L   54 LYS cc_start: 0.8352 (ttmm) cc_final: 0.8021 (tppt)
REVERT: L   62 ARG cc_start: 0.7449 (mmt180) cc_final: 0.6750 (mmp80)
  outliers start: 9
  outliers final: 6
  residues processed: 99
  average time/residue: 0.0816
  time to fit residues: 9.5676
Evaluate side-chains
  100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain L residue   23 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0020
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.102493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.085292 restraints weight = 8991.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 4.21
r_work: 0.3181 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3685  Z= 0.199
  Angle     :  0.755  12.008   5019  Z= 0.377
  Chirality :  0.053   0.531    565
  Planarity :  0.005   0.032    632
  Dihedral  :  6.926  56.752    587
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.02 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.25 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.62 (0.40), residues: 162
  loop : -1.86 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  62 
 TYR   0.013   0.002   TYR B  27 
 PHE   0.017   0.002   PHE A  86 
 TRP   0.010   0.002   TRP B 112 
 HIS   0.005   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 3676)
  covalent geometry    : angle       0.71570 ( 4996)
  SS BOND              : bond        0.00570 (    4)
  SS BOND              : angle       1.58154 (    8)
  hydrogen bonds       : bond        0.04499 (   83)
  hydrogen bonds       : angle       5.92712 (  228)
  link_NAG-ASN         : bond        0.01098 (    5)
  link_NAG-ASN         : angle       4.31017 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.8887 (m-30) cc_final: 0.8682 (m-30)
REVERT: A  153 MET cc_start: 0.8648 (tmm) cc_final: 0.8390 (tmm)
REVERT: A  187 LYS cc_start: 0.7450 (mmmt) cc_final: 0.7189 (mmmt)
REVERT: A  195 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8698 (ttpp)
REVERT: A  202 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8564 (mtpt)
REVERT: B   34 MET cc_start: 0.8688 (tpp) cc_final: 0.8144 (mmm)
REVERT: L   32 ASN cc_start: 0.7570 (m110) cc_final: 0.7291 (m-40)
REVERT: L   33 TYR cc_start: 0.8003 (m-80) cc_final: 0.6787 (m-80)
REVERT: L   54 LYS cc_start: 0.8386 (ttmm) cc_final: 0.8018 (tppt)
  outliers start: 12
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0710
  time to fit residues: 8.8248
Evaluate side-chains
  106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  114 GLN
Chi-restraints excluded: chain L residue   23 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 33 optimal weight:    0.5980
   chunk 11 optimal weight:    0.4980
   chunk 35 optimal weight:    0.1980
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0000
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.3584

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
B 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.103960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.086708 restraints weight = 8878.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 4.20
r_work: 0.3215 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3685  Z= 0.151
  Angle     :  0.742  11.154   5019  Z= 0.366
  Chirality :  0.051   0.481    565
  Planarity :  0.004   0.030    632
  Dihedral  :  6.758  57.598    587
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.05 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.18 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.70 (0.40), residues: 161
  loop : -1.83 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  62 
 TYR   0.010   0.001   TYR B  95 
 PHE   0.011   0.001   PHE A  86 
 TRP   0.008   0.001   TRP A 104 
 HIS   0.002   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3676)
  covalent geometry    : angle       0.70857 ( 4996)
  SS BOND              : bond        0.00489 (    4)
  SS BOND              : angle       1.43454 (    8)
  hydrogen bonds       : bond        0.03845 (   83)
  hydrogen bonds       : angle       5.66731 (  228)
  link_NAG-ASN         : bond        0.01005 (    5)
  link_NAG-ASN         : angle       4.01349 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.8877 (m-30) cc_final: 0.8664 (m-30)
REVERT: A  153 MET cc_start: 0.8664 (tmm) cc_final: 0.8433 (tmm)
REVERT: A  187 LYS cc_start: 0.7454 (mmmt) cc_final: 0.7200 (mmmt)
REVERT: A  202 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8573 (mtpt)
REVERT: B   34 MET cc_start: 0.8661 (tpp) cc_final: 0.7995 (mmm)
REVERT: L   32 ASN cc_start: 0.7499 (m110) cc_final: 0.7246 (m-40)
REVERT: L   33 TYR cc_start: 0.7933 (m-80) cc_final: 0.6814 (m-80)
REVERT: L   76 ILE cc_start: 0.7918 (tp) cc_final: 0.7622 (tt)
  outliers start: 11
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0709
  time to fit residues: 8.7712
Evaluate side-chains
  104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue  107 ASN
Chi-restraints excluded: chain B residue  114 GLN
Chi-restraints excluded: chain L residue   23 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    0.0270
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0770
   chunk 14 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0970
   chunk 7 optimal weight:    0.3980
   chunk 15 optimal weight:    0.3980
   chunk 24 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.1994

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
B 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.105752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.088408 restraints weight = 8833.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 4.24
r_work: 0.3237 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3685  Z= 0.123
  Angle     :  0.738  11.787   5019  Z= 0.362
  Chirality :  0.049   0.439    565
  Planarity :  0.004   0.031    632
  Dihedral  :  6.534  58.714    587
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.31 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.23 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.69 (0.41), residues: 167
  loop : -1.94 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  62 
 TYR   0.009   0.001   TYR A 145 
 PHE   0.009   0.001   PHE B 102 
 TRP   0.009   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3676)
  covalent geometry    : angle       0.70811 ( 4996)
  SS BOND              : bond        0.00389 (    4)
  SS BOND              : angle       1.26526 (    8)
  hydrogen bonds       : bond        0.03229 (   83)
  hydrogen bonds       : angle       5.39055 (  228)
  link_NAG-ASN         : bond        0.00930 (    5)
  link_NAG-ASN         : angle       3.76573 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.8860 (m-30) cc_final: 0.8627 (m-30)
REVERT: A  153 MET cc_start: 0.8632 (tmm) cc_final: 0.8381 (tmm)
REVERT: A  187 LYS cc_start: 0.7369 (mmmt) cc_final: 0.7140 (mmmt)
REVERT: A  202 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8515 (mtpt)
REVERT: B   34 MET cc_start: 0.8622 (tpp) cc_final: 0.7912 (mmm)
REVERT: L   32 ASN cc_start: 0.7500 (m110) cc_final: 0.7003 (m110)
REVERT: L   33 TYR cc_start: 0.7968 (m-80) cc_final: 0.6774 (m-80)
REVERT: L   62 ARG cc_start: 0.7404 (mmt180) cc_final: 0.6677 (mmp80)
REVERT: L   76 ILE cc_start: 0.7791 (tp) cc_final: 0.7516 (tt)
  outliers start: 11
  outliers final: 11
  residues processed: 100
  average time/residue: 0.0833
  time to fit residues: 9.8322
Evaluate side-chains
  103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue  107 ASN
Chi-restraints excluded: chain B residue  114 GLN
Chi-restraints excluded: chain L residue   47 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.099999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.082851 restraints weight = 9000.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 4.20
r_work: 0.3148 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   3685  Z= 0.331
  Angle     :  0.904  13.242   5019  Z= 0.461
  Chirality :  0.058   0.613    565
  Planarity :  0.005   0.036    632
  Dihedral  :  7.282  57.273    587
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 22.11 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.39 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.57 (0.40), residues: 166
  loop : -2.05 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 102 
 TYR   0.021   0.002   TYR B  27 
 PHE   0.023   0.003   PHE A  86 
 TRP   0.012   0.002   TRP B 108 
 HIS   0.006   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00763 ( 3676)
  covalent geometry    : angle       0.86420 ( 4996)
  SS BOND              : bond        0.00750 (    4)
  SS BOND              : angle       2.04511 (    8)
  hydrogen bonds       : bond        0.05888 (   83)
  hydrogen bonds       : angle       6.17140 (  228)
  link_NAG-ASN         : bond        0.01222 (    5)
  link_NAG-ASN         : angle       4.75209 (   15)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8707 (tmm) cc_final: 0.8454 (tmm)
REVERT: A  187 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7317 (mmmt)
REVERT: A  202 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8639 (mtpt)
REVERT: B   34 MET cc_start: 0.8748 (tpp) cc_final: 0.8152 (mmm)
REVERT: L   32 ASN cc_start: 0.7682 (m110) cc_final: 0.7454 (m110)
REVERT: L   33 TYR cc_start: 0.7998 (m-80) cc_final: 0.6728 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 101
  average time/residue: 0.0730
  time to fit residues: 8.8258
Evaluate side-chains
  101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue  107 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    0.2980
   chunk 22 optimal weight:    0.0570
   chunk 33 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    0.4980
   chunk 6 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
** B   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.103027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.085804 restraints weight = 8791.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 4.20
r_work: 0.3202 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3685  Z= 0.166
  Angle     :  0.839  11.621   5019  Z= 0.412
  Chirality :  0.052   0.497    565
  Planarity :  0.005   0.034    632
  Dihedral  :  6.954  57.846    587
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 22.37 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.28 (0.41), residues: 438
  helix:  None (None), residues: 0
  sheet:  0.59 (0.40), residues: 180
  loop : -2.05 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 102 
 TYR   0.012   0.001   TYR A 170 
 PHE   0.012   0.002   PHE B 102 
 TRP   0.009   0.001   TRP B  47 
 HIS   0.003   0.000   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3676)
  covalent geometry    : angle       0.80708 ( 4996)
  SS BOND              : bond        0.00501 (    4)
  SS BOND              : angle       1.46837 (    8)
  hydrogen bonds       : bond        0.04106 (   83)
  hydrogen bonds       : angle       5.92130 (  228)
  link_NAG-ASN         : bond        0.01022 (    5)
  link_NAG-ASN         : angle       4.14593 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1229.32 seconds
wall clock time: 21 minutes 44.85 seconds (1304.85 seconds total)