Starting phenix.real_space_refine
on Tue Mar  3 11:04:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nnz_49589/03_2026/9nnz_49589.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nnz_49589/03_2026/9nnz_49589.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nnz_49589/03_2026/9nnz_49589.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nnz_49589/03_2026/9nnz_49589.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nnz_49589/03_2026/9nnz_49589.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nnz_49589/03_2026/9nnz_49589.cif"
  }
  resolution = 3.94
  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=   0.014
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       9      5.16       5
     C    1621      2.51       5
     N     404      2.21       5
     O     450      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: 2484
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 481
          Classifications: {'peptide': 83}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 175
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 139
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 4, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 4, 'TYR:plan': 4}
          Unresolved non-hydrogen planarities: 97
    Chain: "B"
      Number of atoms: 1936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 1936
          Classifications: {'peptide': 291}
          Incomplete info: {'truncation_to_alanine': 123}
          Link IDs: {'PTRANS': 18, 'TRANS': 272}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 397
          Unresolved non-hydrogen angles: 502
          Unresolved non-hydrogen dihedrals: 313
          Unresolved non-hydrogen chiralities: 55
          Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 7, 'ARG:plan': 5, 'GLN:plan1': 6, 'TYR:plan': 3, 'PHE:plan': 5, 'ASP:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 167
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      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: 0.57, per 1000 atoms: 0.23
  Number of scatterers: 2484
  At special positions: 0
  Unit cell: (46.809, 62.412, 99.562, 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       9     16.00
     O     450      8.00
     N     404      7.00
     C    1621      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 110 " - pdb=" SG  CYS B 187 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG C   1 " - " ASN B  15 "
      " NAG D   1 " - " ASN B   2 "
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 63.5 milliseconds
  

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  698

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 4 sheets defined
      58.8% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'B' and resid 33 through 65
      removed outlier: 3.657A  pdb=" N   LEU B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLY B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   PHE B  52 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      Proline residue:  B  53  - end of helix
    Processing helix  chain 'B' and resid 70 through 90
      removed outlier: 3.746A  pdb=" N   GLY B  90 " --> pdb=" O   MET B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 101
    Processing helix  chain 'B' and resid 106 through 141
    Processing helix  chain 'B' and resid 153 through 174
      Proline residue:  B 170  - end of helix
    Processing helix  chain 'B' and resid 199 through 211
    Processing helix  chain 'B' and resid 212 through 226
      removed outlier: 4.063A  pdb=" N   LEU B 226 " --> pdb=" O   CYS B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 278
      removed outlier: 3.689A  pdb=" N   MET B 253 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   CYS B 264 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
    Processing helix  chain 'B' and resid 284 through 295
      removed outlier: 3.933A  pdb=" N   MET B 288 " --> pdb=" O   GLY B 284 " (cutoff:3.500A)
      Proline residue:  B 291  - end of helix
    Processing helix  chain 'B' and resid 296 through 299
      removed outlier: 4.011A  pdb=" N   ALA B 299 " --> pdb=" O   LYS B 296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 296 through 299'
    Processing helix  chain 'B' and resid 300 through 310
      removed outlier: 4.068A  pdb=" N   VAL B 304 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 320
      removed outlier: 3.598A  pdb=" N   ASN B 315 " --> pdb=" O   LYS B 311 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   CYS B 316 " --> pdb=" O   GLN B 312 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 426
      removed outlier: 4.078A  pdb=" N   SER A 436 " --> pdb=" O   TRP A 423 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ARG A 425 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   TRP A 434 " --> pdb=" O   ARG A 425 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLY A 437 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASP A 446 " --> pdb=" O   GLY A 437 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   TYR A 444 " --> pdb=" O   SER A 439 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 458 through 459
    Processing sheet with id=AA3, first strand: chain 'A' and resid 479 through 480
      removed outlier: 3.659A  pdb=" N   ALA A 479 " --> pdb=" O   VAL A 500 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 178 through 181
      removed outlier: 3.990A  pdb=" N   SER B 186 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)

    159 hydrogen bonds defined for protein.
    471 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: 0.23

  Time building geometry restraints manager: 0.29 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: 775
        1.34 -     1.46: 592
        1.46 -     1.58: 1178
        1.58 -     1.69: 0
        1.69 -     1.81: 13
  Bond restraints: 2558
  Sorted by residual:
  bond pdb=" N   TYR A 486 "
       pdb=" CA  TYR A 486 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.034 1.29e-02 6.01e+03 7.06e+00
  bond pdb=" N   SER A 484 "
       pdb=" CA  SER A 484 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.25e-02 6.40e+03 6.34e+00
  bond pdb=" N   ASN B   2 "
       pdb=" CA  ASN B   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.30e-02 5.92e+03 5.96e+00
  bond pdb=" N   PHE B 116 "
       pdb=" CA  PHE B 116 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.19e-02 7.06e+03 5.83e+00
  bond pdb=" CA  GLU B 201 "
       pdb=" C   GLU B 201 "
    ideal  model  delta    sigma   weight residual
    1.524  1.496  0.028 1.24e-02 6.50e+03 5.08e+00
  ... (remaining 2553 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 3279
        1.18 -     2.36: 182
        2.36 -     3.54: 48
        3.54 -     4.71: 18
        4.71 -     5.89: 6
  Bond angle restraints: 3533
  Sorted by residual:
  angle pdb=" C   ARG A 440 "
        pdb=" CA  ARG A 440 "
        pdb=" CB  ARG A 440 "
      ideal   model   delta    sigma   weight residual
     116.63  111.43    5.20 1.16e+00 7.43e-01 2.01e+01
  angle pdb=" CA  ARG A 440 "
        pdb=" C   ARG A 440 "
        pdb=" N   ASP A 441 "
      ideal   model   delta    sigma   weight residual
     119.63  116.59    3.04 8.10e-01 1.52e+00 1.41e+01
  angle pdb=" C   VAL B 209 "
        pdb=" N   VAL B 210 "
        pdb=" CA  VAL B 210 "
      ideal   model   delta    sigma   weight residual
     121.84  117.62    4.22 1.13e+00 7.83e-01 1.40e+01
  angle pdb=" CA  LYS A 485 "
        pdb=" C   LYS A 485 "
        pdb=" O   LYS A 485 "
      ideal   model   delta    sigma   weight residual
     122.01  118.17    3.84 1.05e+00 9.07e-01 1.33e+01
  angle pdb=" N   GLU B 201 "
        pdb=" CA  GLU B 201 "
        pdb=" C   GLU B 201 "
      ideal   model   delta    sigma   weight residual
     110.97  107.40    3.57 1.09e+00 8.42e-01 1.07e+01
  ... (remaining 3528 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.02: 1384
       21.02 -    42.04: 66
       42.04 -    63.06: 10
       63.06 -    84.08: 7
       84.08 -   105.11: 4
  Dihedral angle restraints: 1471
    sinusoidal: 390
      harmonic: 1081
  Sorted by residual:
  dihedral pdb=" CB  CYS B 110 "
           pdb=" SG  CYS B 110 "
           pdb=" SG  CYS B 187 "
           pdb=" CB  CYS B 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.04   35.04     1      1.00e+01 1.00e-02 1.74e+01
  dihedral pdb=" O4  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -176.40  105.11     1      3.00e+01 1.11e-03 1.34e+01
  dihedral pdb=" C3  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -55.56  103.18     1      3.00e+01 1.11e-03 1.31e+01
  ... (remaining 1468 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 403
       0.099 -    0.198: 13
       0.198 -    0.297: 1
       0.297 -    0.396: 0
       0.396 -    0.496: 1
  Chirality restraints: 418
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-02 2.50e+03 8.00e+01
  chirality pdb=" C1  BMA C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.33   -0.07 2.00e-02 2.50e+03 1.29e+01
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B   2 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.90   -0.50 2.00e-01 2.50e+01 6.14e+00
  ... (remaining 415 not shown)

  Planarity restraints: 458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "    0.346 2.00e-02 2.50e+03   2.97e-01 1.10e+03
        pdb=" C7  NAG D   1 "   -0.086 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "    0.146 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "   -0.527 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.121 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.233 2.00e-02 2.50e+03   1.95e-01 4.73e+02
        pdb=" C7  NAG D   2 "    0.062 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.162 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.323 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "   -0.096 2.00e-02 2.50e+03   8.13e-02 8.26e+01
        pdb=" C7  NAG C   1 "    0.022 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.023 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "    0.129 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "   -0.078 2.00e-02 2.50e+03
  ... (remaining 455 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.01: 1382
        3.01 -     3.48: 2509
        3.48 -     3.95: 3615
        3.95 -     4.43: 3944
        4.43 -     4.90: 6221
  Nonbonded interactions: 17671
  Sorted by model distance:
  nonbonded pdb=" O5  NAG D   2 "
            pdb=" O6  NAG D   2 "
     model   vdw
     2.532 2.432
  nonbonded pdb=" OG  SER A 488 "
            pdb=" N   THR A 491 "
     model   vdw
     2.555 3.120
  nonbonded pdb=" OE1 GLU B 201 "
            pdb=" N   SER B 202 "
     model   vdw
     2.568 3.120
  nonbonded pdb=" O3  NAG D   1 "
            pdb=" O5  NAG D   2 "
     model   vdw
     2.573 3.040
  nonbonded pdb=" N   LYS A 485 "
            pdb=" O   LYS A 485 "
     model   vdw
     2.604 2.496
  ... (remaining 17666 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:             0.920
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     3.770
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6607
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      :  0.005   0.047   2564  Z= 0.275
  Angle     :  0.771   9.921   3550  Z= 0.433
  Chirality :  0.051   0.496    418
  Planarity :  0.018   0.297    456
  Dihedral  : 15.456 105.105    770
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.72 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.44), residues: 356
  helix:  1.56 (0.36), residues: 202
  sheet: -3.14 (1.01), residues: 17
  loop : -2.17 (0.48), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG B 177 
 TYR   0.016   0.001   TYR B  43 
 PHE   0.008   0.001   PHE B  24 
 TRP   0.019   0.002   TRP B 175 
 HIS   0.003   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 2558)
  covalent geometry    : angle       0.71752 ( 3533)
  SS BOND              : bond        0.00337 (    1)
  SS BOND              : angle       0.17610 (    2)
  hydrogen bonds       : bond        0.13658 (  159)
  hydrogen bonds       : angle       5.67741 (  471)
  link_BETA1-4         : bond        0.04683 (    3)
  link_BETA1-4         : angle       5.22075 (    9)
  link_NAG-ASN         : bond        0.00828 (    2)
  link_NAG-ASN         : angle       2.73251 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.083 
Fit side-chains
REVERT: B   47 LEU cc_start: 0.8623 (tp) cc_final: 0.8048 (mt)
REVERT: B  185 CYS cc_start: 0.8027 (m) cc_final: 0.7573 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0236
  time to fit residues: 2.1360
Evaluate side-chains
  42 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.147028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.127302 restraints weight = 4801.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130392 restraints weight = 2766.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.132699 restraints weight = 1872.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.134289 restraints weight = 1380.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.135295 restraints weight = 1097.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2564  Z= 0.138
  Angle     :  0.695  11.921   3550  Z= 0.322
  Chirality :  0.048   0.254    418
  Planarity :  0.004   0.033    456
  Dihedral  :  9.200  62.686    487
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 22.76 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.45), residues: 356
  helix:  2.14 (0.35), residues: 208
  sheet: -5.19 (0.95), residues: 6
  loop : -2.01 (0.49), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 177 
 TYR   0.018   0.001   TYR B 206 
 PHE   0.027   0.002   PHE B 203 
 TRP   0.008   0.001   TRP B 175 
 HIS   0.003   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 2558)
  covalent geometry    : angle       0.67291 ( 3533)
  SS BOND              : bond        0.00351 (    1)
  SS BOND              : angle       3.00933 (    2)
  hydrogen bonds       : bond        0.03369 (  159)
  hydrogen bonds       : angle       4.16862 (  471)
  link_BETA1-4         : bond        0.00507 (    3)
  link_BETA1-4         : angle       2.36879 (    9)
  link_NAG-ASN         : bond        0.00467 (    2)
  link_NAG-ASN         : angle       2.82293 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.082 
Fit side-chains
REVERT: B   44 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7400 (tpp)
REVERT: B   47 LEU cc_start: 0.8809 (tp) cc_final: 0.8216 (mt)
REVERT: B  184 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8828 (mm-40)
REVERT: B  313 PHE cc_start: 0.8697 (t80) cc_final: 0.8304 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 43
  average time/residue: 0.0200
  time to fit residues: 1.3607
Evaluate side-chains
  43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  129 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   chunk 18 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 100 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.139716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.119969 restraints weight = 4970.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.122949 restraints weight = 2924.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.124993 restraints weight = 1998.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.126342 restraints weight = 1516.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.127135 restraints weight = 1238.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2564  Z= 0.126
  Angle     :  0.570   6.026   3550  Z= 0.277
  Chirality :  0.042   0.178    418
  Planarity :  0.004   0.035    456
  Dihedral  :  4.574  20.759    487
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 17.24 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.46), residues: 356
  helix:  2.50 (0.36), residues: 207
  sheet: -0.41 (1.79), residues: 7
  loop : -1.95 (0.50), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 177 
 TYR   0.014   0.001   TYR B 206 
 PHE   0.014   0.001   PHE B 203 
 TRP   0.005   0.001   TRP B 161 
 HIS   0.004   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 2558)
  covalent geometry    : angle       0.55172 ( 3533)
  SS BOND              : bond        0.00801 (    1)
  SS BOND              : angle       1.96989 (    2)
  hydrogen bonds       : bond        0.03509 (  159)
  hydrogen bonds       : angle       3.74644 (  471)
  link_BETA1-4         : bond        0.00463 (    3)
  link_BETA1-4         : angle       2.45145 (    9)
  link_NAG-ASN         : bond        0.00418 (    2)
  link_NAG-ASN         : angle       1.62528 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.085 
Fit side-chains
REVERT: B   79 LEU cc_start: 0.9154 (mm) cc_final: 0.8943 (mt)
  outliers start: 7
  outliers final: 3
  residues processed: 48
  average time/residue: 0.0224
  time to fit residues: 1.6417
Evaluate side-chains
  44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue  129 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0050
   chunk 32 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
B 100 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.117371 restraints weight = 5043.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.120332 restraints weight = 2918.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.122381 restraints weight = 1978.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.123760 restraints weight = 1488.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.124547 restraints weight = 1219.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2564  Z= 0.113
  Angle     :  0.547   6.160   3550  Z= 0.266
  Chirality :  0.043   0.214    418
  Planarity :  0.004   0.035    456
  Dihedral  :  3.968  19.079    487
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 18.62 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.46), residues: 356
  helix:  2.48 (0.36), residues: 208
  sheet: -0.90 (1.25), residues: 22
  loop : -2.12 (0.52), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 177 
 TYR   0.013   0.001   TYR B 206 
 PHE   0.013   0.001   PHE B 203 
 TRP   0.004   0.001   TRP B  35 
 HIS   0.004   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 2558)
  covalent geometry    : angle       0.53490 ( 3533)
  SS BOND              : bond        0.00462 (    1)
  SS BOND              : angle       1.90447 (    2)
  hydrogen bonds       : bond        0.03223 (  159)
  hydrogen bonds       : angle       3.72999 (  471)
  link_BETA1-4         : bond        0.00365 (    3)
  link_BETA1-4         : angle       1.79900 (    9)
  link_NAG-ASN         : bond        0.00268 (    2)
  link_NAG-ASN         : angle       1.58901 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.086 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 42
  average time/residue: 0.0223
  time to fit residues: 1.4596
Evaluate side-chains
  43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  193 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0270
   chunk 3 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8642

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.133334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.113634 restraints weight = 5154.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.116555 restraints weight = 3034.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118450 restraints weight = 2066.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.119879 restraints weight = 1560.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.121018 restraints weight = 1253.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2564  Z= 0.127
  Angle     :  0.546   5.935   3550  Z= 0.269
  Chirality :  0.042   0.219    418
  Planarity :  0.004   0.036    456
  Dihedral  :  3.789  17.933    487
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.31 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.46), residues: 356
  helix:  2.52 (0.35), residues: 208
  sheet: -0.61 (1.24), residues: 22
  loop : -2.08 (0.51), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 177 
 TYR   0.010   0.001   TYR B 206 
 PHE   0.009   0.001   PHE B 203 
 TRP   0.005   0.001   TRP B  35 
 HIS   0.005   0.002   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 2558)
  covalent geometry    : angle       0.53551 ( 3533)
  SS BOND              : bond        0.00643 (    1)
  SS BOND              : angle       1.79926 (    2)
  hydrogen bonds       : bond        0.03635 (  159)
  hydrogen bonds       : angle       3.73205 (  471)
  link_BETA1-4         : bond        0.00364 (    3)
  link_BETA1-4         : angle       1.67739 (    9)
  link_NAG-ASN         : bond        0.00217 (    2)
  link_NAG-ASN         : angle       1.45339 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.083 
Fit side-chains
REVERT: B   44 MET cc_start: 0.8315 (tpp) cc_final: 0.8079 (tpt)
  outliers start: 5
  outliers final: 4
  residues processed: 40
  average time/residue: 0.0230
  time to fit residues: 1.4611
Evaluate side-chains
  40 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  193 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 1 optimal weight:    0.0870
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6760

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.134160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.114647 restraints weight = 5110.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.117462 restraints weight = 3016.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.119527 restraints weight = 2058.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.120844 restraints weight = 1542.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.121667 restraints weight = 1258.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.4385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2564  Z= 0.106
  Angle     :  0.528   6.484   3550  Z= 0.257
  Chirality :  0.042   0.212    418
  Planarity :  0.004   0.038    456
  Dihedral  :  3.633  16.584    487
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.07 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.46), residues: 356
  helix:  2.64 (0.36), residues: 208
  sheet: -0.06 (1.26), residues: 22
  loop : -2.03 (0.50), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 177 
 TYR   0.011   0.001   TYR B 206 
 PHE   0.010   0.001   PHE B 203 
 TRP   0.005   0.001   TRP A 434 
 HIS   0.003   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 2558)
  covalent geometry    : angle       0.51850 ( 3533)
  SS BOND              : bond        0.00462 (    1)
  SS BOND              : angle       1.71014 (    2)
  hydrogen bonds       : bond        0.03187 (  159)
  hydrogen bonds       : angle       3.62281 (  471)
  link_BETA1-4         : bond        0.00338 (    3)
  link_BETA1-4         : angle       1.51299 (    9)
  link_NAG-ASN         : bond        0.00247 (    2)
  link_NAG-ASN         : angle       1.48584 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.085 
Fit side-chains
REVERT: B   44 MET cc_start: 0.8390 (tpp) cc_final: 0.8164 (tpt)
  outliers start: 5
  outliers final: 5
  residues processed: 42
  average time/residue: 0.0188
  time to fit residues: 1.2425
Evaluate side-chains
  41 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  193 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 10 optimal weight:    0.0270
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.4438

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.135197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.115766 restraints weight = 5066.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.118716 restraints weight = 3006.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.120627 restraints weight = 2039.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122096 restraints weight = 1533.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.123106 restraints weight = 1244.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.4416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2564  Z= 0.096
  Angle     :  0.521   6.372   3550  Z= 0.253
  Chirality :  0.041   0.204    418
  Planarity :  0.004   0.038    456
  Dihedral  :  3.530  16.649    487
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.76 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.46), residues: 356
  helix:  2.71 (0.35), residues: 209
  sheet:  0.08 (1.25), residues: 22
  loop : -1.96 (0.51), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 177 
 TYR   0.010   0.001   TYR B 206 
 PHE   0.009   0.001   PHE B 203 
 TRP   0.005   0.001   TRP A 434 
 HIS   0.001   0.000   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 2558)
  covalent geometry    : angle       0.51240 ( 3533)
  SS BOND              : bond        0.00343 (    1)
  SS BOND              : angle       1.62263 (    2)
  hydrogen bonds       : bond        0.03005 (  159)
  hydrogen bonds       : angle       3.55839 (  471)
  link_BETA1-4         : bond        0.00377 (    3)
  link_BETA1-4         : angle       1.50939 (    9)
  link_NAG-ASN         : bond        0.00255 (    2)
  link_NAG-ASN         : angle       1.40507 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.087 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 41
  average time/residue: 0.0215
  time to fit residues: 1.3347
Evaluate side-chains
  41 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  129 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B 100 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.128964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109643 restraints weight = 5312.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.112409 restraints weight = 3154.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.114203 restraints weight = 2155.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.115479 restraints weight = 1635.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.115894 restraints weight = 1350.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.4834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2564  Z= 0.161
  Angle     :  0.586   5.860   3550  Z= 0.295
  Chirality :  0.044   0.230    418
  Planarity :  0.004   0.037    456
  Dihedral  :  3.703  18.723    487
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 21.38 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.46), residues: 356
  helix:  2.52 (0.35), residues: 209
  sheet:  0.30 (1.21), residues: 22
  loop : -1.98 (0.52), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 177 
 TYR   0.008   0.001   TYR B 206 
 PHE   0.010   0.001   PHE B 273 
 TRP   0.008   0.001   TRP B 265 
 HIS   0.003   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 2558)
  covalent geometry    : angle       0.57684 ( 3533)
  SS BOND              : bond        0.00669 (    1)
  SS BOND              : angle       1.75107 (    2)
  hydrogen bonds       : bond        0.04236 (  159)
  hydrogen bonds       : angle       3.94919 (  471)
  link_BETA1-4         : bond        0.00338 (    3)
  link_BETA1-4         : angle       1.61348 (    9)
  link_NAG-ASN         : bond        0.00199 (    2)
  link_NAG-ASN         : angle       1.52029 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.095 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 43
  average time/residue: 0.0247
  time to fit residues: 1.6511
Evaluate side-chains
  39 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  193 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0770
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 = 0.3531 r_free = 0.3531 target = 0.131847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.112533 restraints weight = 5240.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.115318 restraints weight = 3095.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.117163 restraints weight = 2112.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.118484 restraints weight = 1607.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.119516 restraints weight = 1317.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.4898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2564  Z= 0.109
  Angle     :  0.552   6.450   3550  Z= 0.268
  Chirality :  0.043   0.216    418
  Planarity :  0.004   0.038    456
  Dihedral  :  3.641  17.770    487
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.07 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.46), residues: 356
  helix:  2.53 (0.35), residues: 209
  sheet:  0.50 (1.22), residues: 22
  loop : -1.90 (0.52), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 177 
 TYR   0.010   0.001   TYR B 206 
 PHE   0.011   0.001   PHE B  91 
 TRP   0.007   0.001   TRP A 434 
 HIS   0.005   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 2558)
  covalent geometry    : angle       0.54369 ( 3533)
  SS BOND              : bond        0.00475 (    1)
  SS BOND              : angle       1.59801 (    2)
  hydrogen bonds       : bond        0.03496 (  159)
  hydrogen bonds       : angle       3.69524 (  471)
  link_BETA1-4         : bond        0.00362 (    3)
  link_BETA1-4         : angle       1.48416 (    9)
  link_NAG-ASN         : bond        0.00269 (    2)
  link_NAG-ASN         : angle       1.54543 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.057 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 42
  average time/residue: 0.0224
  time to fit residues: 1.4616
Evaluate side-chains
  43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  193 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.130593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.111183 restraints weight = 5167.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114029 restraints weight = 3045.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.115987 restraints weight = 2061.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.117234 restraints weight = 1551.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.118223 restraints weight = 1273.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2564  Z= 0.124
  Angle     :  0.570   7.349   3550  Z= 0.275
  Chirality :  0.043   0.217    418
  Planarity :  0.004   0.038    456
  Dihedral  :  3.604  18.313    487
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 22.76 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.46), residues: 356
  helix:  2.52 (0.35), residues: 209
  sheet:  0.44 (1.22), residues: 22
  loop : -1.92 (0.52), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 177 
 TYR   0.009   0.001   TYR B 206 
 PHE   0.013   0.001   PHE B  91 
 TRP   0.005   0.001   TRP A 434 
 HIS   0.005   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 2558)
  covalent geometry    : angle       0.56182 ( 3533)
  SS BOND              : bond        0.00412 (    1)
  SS BOND              : angle       1.57526 (    2)
  hydrogen bonds       : bond        0.03573 (  159)
  hydrogen bonds       : angle       3.73720 (  471)
  link_BETA1-4         : bond        0.00376 (    3)
  link_BETA1-4         : angle       1.51182 (    9)
  link_NAG-ASN         : bond        0.00226 (    2)
  link_NAG-ASN         : angle       1.51151 (    6)

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.076 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 43
  average time/residue: 0.0234
  time to fit residues: 1.5528
Evaluate side-chains
  46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  193 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3528 r_free = 0.3528 target = 0.131686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.112167 restraints weight = 5210.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.115044 restraints weight = 3072.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.116934 restraints weight = 2084.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.118312 restraints weight = 1583.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.119397 restraints weight = 1285.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2564  Z= 0.112
  Angle     :  0.556   7.613   3550  Z= 0.267
  Chirality :  0.043   0.213    418
  Planarity :  0.004   0.039    456
  Dihedral  :  3.586  18.122    487
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.45 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.46), residues: 356
  helix:  2.51 (0.35), residues: 209
  sheet:  0.64 (1.27), residues: 22
  loop : -1.82 (0.53), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 177 
 TYR   0.010   0.001   TYR B 206 
 PHE   0.014   0.001   PHE B  91 
 TRP   0.008   0.001   TRP A 434 
 HIS   0.005   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 2558)
  covalent geometry    : angle       0.54812 ( 3533)
  SS BOND              : bond        0.00356 (    1)
  SS BOND              : angle       1.59213 (    2)
  hydrogen bonds       : bond        0.03354 (  159)
  hydrogen bonds       : angle       3.70000 (  471)
  link_BETA1-4         : bond        0.00376 (    3)
  link_BETA1-4         : angle       1.44253 (    9)
  link_NAG-ASN         : bond        0.00237 (    2)
  link_NAG-ASN         : angle       1.50879 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 546.15 seconds
wall clock time: 9 minutes 59.71 seconds (599.71 seconds total)