Starting phenix.real_space_refine
on Fri Aug 22 18:47:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dtk_27703/08_2025/8dtk_27703_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dtk_27703/08_2025/8dtk_27703.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dtk_27703/08_2025/8dtk_27703.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dtk_27703/08_2025/8dtk_27703.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dtk_27703/08_2025/8dtk_27703_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dtk_27703/08_2025/8dtk_27703_neut_trim.cif"
  }
  resolution = 3.77
  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=  -0.004 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2248      2.51       5
     N     596      2.21       5
     O     692      1.98       5
     H    3363      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6914
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 3134
          Classifications: {'peptide': 203}
          Modifications used: {'NH2': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 191}
    Chain: "B"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 1749
          Classifications: {'peptide': 113}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 106}
    Chain: "C"
      Number of atoms: 2003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 2003
          Classifications: {'peptide': 133}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 129}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.47, per 1000 atoms: 0.21
  Number of scatterers: 6914
  At special positions: 0
  Unit cell: (69.828, 92.046, 85.698, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     O     692      8.00
     N     596      7.00
     C    2248      6.00
     H    3363      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " 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
    NAG-ASN
      " NAG A 601 " - " ASN A 331 "
      " NAG A 602 " - " ASN A 343 "
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 287.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 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:
      9 helices and 9 sheets defined
      11.4% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 384 through 390
      removed outlier: 3.753A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.151A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'C' and resid 61 through 64
      removed outlier: 3.571A  pdb=" N   GLN C  64 " --> pdb=" O   GLN C  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 61 through 64'
    Processing helix  chain 'C' and resid 83 through 87
      removed outlier: 3.666A  pdb=" N   THR C  87 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.909A  pdb=" N   LYS A 356 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   ASN A 437 " --> pdb=" O   PHE A 374 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   PHE A 374 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.909A  pdb=" N   LYS A 356 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.853A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 5
      removed outlier: 3.839A  pdb=" N   THR B   5 " --> pdb=" O   ARG B  24 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ARG B  24 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ASP B  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER B  67 " --> pdb=" O   ASP B  70 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.551A  pdb=" N   VAL B  85 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6
      removed outlier: 3.968A  pdb=" N   VAL C   5 " --> pdb=" O   GLN C  23 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLN C  23 " --> pdb=" O   VAL C   5 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE C  78 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.637A  pdb=" N   GLU C  10 " --> pdb=" O   LEU C 108 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR C 110 " --> pdb=" O   GLU C  10 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ILE C  34 " --> pdb=" O   ILE C  50 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   TRP C  36 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 18
      removed outlier: 3.543A  pdb=" N   VAL C  18 " --> pdb=" O   LEU C  82 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU C  82 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    78 hydrogen bonds defined for protein.
    177 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3363
        1.03 -     1.23: 9
        1.23 -     1.42: 1608
        1.42 -     1.62: 2005
        1.62 -     1.81: 18
  Bond restraints: 7003
  Sorted by residual:
  bond pdb=" CB  GLU C  81 "
       pdb=" CG  GLU C  81 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.12e+00
  bond pdb=" CB  ASP C  95 "
       pdb=" CG  ASP C  95 "
    ideal  model  delta    sigma   weight residual
    1.516  1.484  0.032 2.50e-02 1.60e+03 1.66e+00
  bond pdb=" CB  ASP B   9 "
       pdb=" CG  ASP B   9 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.56e+00
  bond pdb=" C5  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.46e+00
  bond pdb=" CB  MET B   4 "
       pdb=" CG  MET B   4 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.34e+00
  ... (remaining 6998 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.57: 12528
        7.57 -    15.13: 2
       15.13 -    22.70: 1
       22.70 -    30.26: 2
       30.26 -    37.83: 3
  Bond angle restraints: 12536
  Sorted by residual:
  angle pdb=" C   PHE C 100N"
        pdb=" CA  PHE C 100N"
        pdb=" HA  PHE C 100N"
      ideal   model   delta    sigma   weight residual
     109.00   71.17   37.83 3.00e+00 1.11e-01 1.59e+02
  angle pdb=" N   PHE C 100N"
        pdb=" CA  PHE C 100N"
        pdb=" HA  PHE C 100N"
      ideal   model   delta    sigma   weight residual
     110.00   74.48   35.52 3.00e+00 1.11e-01 1.40e+02
  angle pdb=" CB  PHE C 100N"
        pdb=" CA  PHE C 100N"
        pdb=" HA  PHE C 100N"
      ideal   model   delta    sigma   weight residual
     109.00   78.57   30.43 3.00e+00 1.11e-01 1.03e+02
  angle pdb=" CB  LEU C   4 "
        pdb=" CG  LEU C   4 "
        pdb=" HG  LEU C   4 "
      ideal   model   delta    sigma   weight residual
     109.00   85.17   23.83 3.00e+00 1.11e-01 6.31e+01
  angle pdb=" CD2 LEU C   4 "
        pdb=" CG  LEU C   4 "
        pdb=" HG  LEU C   4 "
      ideal   model   delta    sigma   weight residual
     108.00   84.21   23.79 3.00e+00 1.11e-01 6.29e+01
  ... (remaining 12531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.08: 3126
       22.08 -    44.16: 208
       44.16 -    66.23: 51
       66.23 -    88.31: 15
       88.31 -   110.39: 5
  Dihedral angle restraints: 3405
    sinusoidal: 1818
      harmonic: 1587
  Sorted by residual:
  dihedral pdb=" CA  CYS A 391 "
           pdb=" C   CYS A 391 "
           pdb=" N   PHE A 392 "
           pdb=" CA  PHE A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.19  -25.81     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  VAL A 524 "
           pdb=" C   VAL A 524 "
           pdb=" N   CYS A 525 "
           pdb=" CA  CYS A 525 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.80  -24.20     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  92 "
           pdb=" CB  CYS C  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  125.03  -32.03     1      1.00e+01 1.00e-02 1.46e+01
  ... (remaining 3402 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.352: 537
       0.352 -    0.705: 0
       0.705 -    1.057: 0
       1.057 -    1.409: 0
       1.409 -    1.762: 1
  Chirality restraints: 538
  Sorted by residual:
  chirality pdb=" CG  LEU C   4 "
            pdb=" CB  LEU C   4 "
            pdb=" CD1 LEU C   4 "
            pdb=" CD2 LEU C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.83   -1.76 2.00e-01 2.50e+01 7.76e+01
  chirality pdb=" CA  PHE C 100N"
            pdb=" N   PHE C 100N"
            pdb=" C   PHE C 100N"
            pdb=" CB  PHE C 100N"
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.49e+00
  chirality pdb=" CA  ILE B  48 "
            pdb=" N   ILE B  48 "
            pdb=" C   ILE B  48 "
            pdb=" CB  ILE B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.28e-01
  ... (remaining 535 not shown)

  Planarity restraints: 1068
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  61 "    0.214 9.50e-02 1.11e+02   7.17e-02 6.49e+00
        pdb=" NE  ARG B  61 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  61 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  61 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  61 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG B  61 "   -0.005 2.00e-02 2.50e+03
        pdb="HH12 ARG B  61 "    0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG B  61 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG B  61 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 497 "    0.013 2.00e-02 2.50e+03   1.04e-02 3.23e+00
        pdb=" CG  PHE A 497 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 497 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 497 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 497 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 497 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 497 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 497 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 497 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 497 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 497 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 497 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  13 "    0.028 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO C  14 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO C  14 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  14 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1065 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 838
        2.24 -     2.83: 14848
        2.83 -     3.42: 17054
        3.42 -     4.01: 23693
        4.01 -     4.60: 35931
  Nonbonded interactions: 92364
  Sorted by model distance:
  nonbonded pdb=" H   PHE C 100N"
            pdb=" HA  PHE C 100N"
     model   vdw
     1.653 1.816
  nonbonded pdb=" HA  PHE C 100N"
            pdb=" HB2 PHE C 100N"
     model   vdw
     1.710 1.952
  nonbonded pdb=" H   ALA A 363 "
            pdb=" O   CYS A 525 "
     model   vdw
     1.732 2.450
  nonbonded pdb="HH12 ARG A 454 "
            pdb=" O   SER A 469 "
     model   vdw
     1.739 2.450
  nonbonded pdb=" O   VAL C  96 "
            pdb=" HG1 THR C 100L"
     model   vdw
     1.744 2.450
  ... (remaining 92359 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:             2.730
  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:             0.040
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.300
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
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   0.044   3648  Z= 0.200
  Angle     :  0.794  10.998   4971  Z= 0.416
  Chirality :  0.091   1.762    538
  Planarity :  0.006   0.095    640
  Dihedral  : 16.060 110.391   1326
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.29 (0.37), residues: 443
  helix: -3.24 (0.52), residues: 40
  sheet: -1.95 (0.44), residues: 124
  loop : -1.00 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B  61 
 TYR   0.021   0.002   TYR B  49 
 PHE   0.031   0.002   PHE A 497 
 TRP   0.024   0.002   TRP C 100B
 HIS   0.005   0.002   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 3640)
  covalent geometry    : angle       0.78779 ( 4953)
  SS BOND              : bond        0.00468 (    6)
  SS BOND              : angle       1.42222 (   12)
  hydrogen bonds       : bond        0.31874 (   73)
  hydrogen bonds       : angle      11.46960 (  177)
  link_NAG-ASN         : bond        0.00070 (    2)
  link_NAG-ASN         : angle       2.53463 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1593
  time to fit residues: 16.1298
Evaluate side-chains
  69 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.1980
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
B  42 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.189376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.167855 restraints weight = 11700.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.173615 restraints weight = 6230.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.177312 restraints weight = 3962.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.179670 restraints weight = 2801.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.181459 restraints weight = 2135.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3648  Z= 0.144
  Angle     :  0.638  10.366   4971  Z= 0.325
  Chirality :  0.089   1.734    538
  Planarity :  0.004   0.040    640
  Dihedral  :  8.459  58.629    541
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  7.79 %
    Favored  : 91.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.19 (0.37), residues: 443
  helix: -3.08 (0.60), residues: 40
  sheet: -1.93 (0.45), residues: 124
  loop : -0.90 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  71 
 TYR   0.013   0.001   TYR B  49 
 PHE   0.015   0.001   PHE A 490 
 TRP   0.008   0.001   TRP C 100B
 HIS   0.002   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3640)
  covalent geometry    : angle       0.63414 ( 4953)
  SS BOND              : bond        0.00432 (    6)
  SS BOND              : angle       0.81007 (   12)
  hydrogen bonds       : bond        0.05185 (   73)
  hydrogen bonds       : angle       7.58516 (  177)
  link_NAG-ASN         : bond        0.00090 (    2)
  link_NAG-ASN         : angle       1.92649 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 LYS cc_start: 0.7114 (tmtt) cc_final: 0.6761 (tmtt)
  outliers start: 2
  outliers final: 2
  residues processed: 74
  average time/residue: 0.1630
  time to fit residues: 14.6534
Evaluate side-chains
  72 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 35 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 334 ASN
B  27 GLN
B  42 GLN
C   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.182140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.159850 restraints weight = 11954.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.165441 restraints weight = 6575.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.169140 restraints weight = 4275.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.171478 restraints weight = 3097.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.173182 restraints weight = 2418.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3648  Z= 0.149
  Angle     :  0.590  10.271   4971  Z= 0.302
  Chirality :  0.088   1.735    538
  Planarity :  0.004   0.046    640
  Dihedral  :  7.063  49.189    541
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.83 %
    Favored  : 89.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.22 (0.37), residues: 443
  helix: -3.22 (0.57), residues: 40
  sheet: -1.84 (0.48), residues: 108
  loop : -1.05 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 454 
 TYR   0.014   0.001   TYR B  49 
 PHE   0.010   0.001   PHE A 429 
 TRP   0.005   0.001   TRP B  35 
 HIS   0.004   0.002   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 3640)
  covalent geometry    : angle       0.58583 ( 4953)
  SS BOND              : bond        0.00435 (    6)
  SS BOND              : angle       0.84956 (   12)
  hydrogen bonds       : bond        0.04219 (   73)
  hydrogen bonds       : angle       6.79761 (  177)
  link_NAG-ASN         : bond        0.00215 (    2)
  link_NAG-ASN         : angle       1.96254 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 77
  average time/residue: 0.1963
  time to fit residues: 17.8420
Evaluate side-chains
  73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  42 GLN
C   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.178368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156292 restraints weight = 12211.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.161750 restraints weight = 6834.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.165330 restraints weight = 4489.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.167724 restraints weight = 3273.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.169254 restraints weight = 2552.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3648  Z= 0.169
  Angle     :  0.598  11.598   4971  Z= 0.306
  Chirality :  0.088   1.749    538
  Planarity :  0.004   0.043    640
  Dihedral  :  6.601  53.674    541
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 11.95 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.22 (0.38), residues: 443
  helix: -2.92 (0.69), residues: 33
  sheet: -1.92 (0.48), residues: 108
  loop : -1.12 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  71 
 TYR   0.013   0.001   TYR B  49 
 PHE   0.010   0.001   PHE A 429 
 TRP   0.005   0.001   TRP C  47 
 HIS   0.003   0.002   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3640)
  covalent geometry    : angle       0.58824 ( 4953)
  SS BOND              : bond        0.00525 (    6)
  SS BOND              : angle       0.89235 (   12)
  hydrogen bonds       : bond        0.03611 (   73)
  hydrogen bonds       : angle       6.40301 (  177)
  link_NAG-ASN         : bond        0.00403 (    2)
  link_NAG-ASN         : angle       2.98706 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 78
  average time/residue: 0.1902
  time to fit residues: 17.6493
Evaluate side-chains
  72 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain C residue    3 GLN
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 6 optimal weight:    0.1980
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.182454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.160441 restraints weight = 11990.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.166097 restraints weight = 6576.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.169702 restraints weight = 4257.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.171802 restraints weight = 3065.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.173544 restraints weight = 2430.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3648  Z= 0.138
  Angle     :  0.581  11.143   4971  Z= 0.295
  Chirality :  0.087   1.734    538
  Planarity :  0.004   0.052    640
  Dihedral  :  6.423  52.193    541
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 12.99 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.18 (0.38), residues: 443
  helix: -2.88 (0.69), residues: 33
  sheet: -1.82 (0.48), residues: 109
  loop : -1.13 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  61 
 TYR   0.014   0.001   TYR B  49 
 PHE   0.009   0.001   PHE C  29 
 TRP   0.005   0.001   TRP C 100B
 HIS   0.003   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3640)
  covalent geometry    : angle       0.57221 ( 4953)
  SS BOND              : bond        0.00453 (    6)
  SS BOND              : angle       0.80277 (   12)
  hydrogen bonds       : bond        0.03335 (   73)
  hydrogen bonds       : angle       6.18935 (  177)
  link_NAG-ASN         : bond        0.00281 (    2)
  link_NAG-ASN         : angle       2.86766 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 75
  average time/residue: 0.1854
  time to fit residues: 16.5669
Evaluate side-chains
  73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 2 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.2980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.181677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.159659 restraints weight = 12040.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.165284 restraints weight = 6603.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.168392 restraints weight = 4276.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.171086 restraints weight = 3173.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.172799 restraints weight = 2446.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3648  Z= 0.139
  Angle     :  0.582  10.590   4971  Z= 0.294
  Chirality :  0.091   1.831    538
  Planarity :  0.004   0.057    640
  Dihedral  :  6.319  52.566    541
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.03 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.11 (0.38), residues: 443
  helix: -2.78 (0.71), residues: 33
  sheet: -1.73 (0.48), residues: 109
  loop : -1.11 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  61 
 TYR   0.014   0.001   TYR B  49 
 PHE   0.007   0.001   PHE A 490 
 TRP   0.004   0.001   TRP C 103 
 HIS   0.002   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3640)
  covalent geometry    : angle       0.57082 ( 4953)
  SS BOND              : bond        0.00477 (    6)
  SS BOND              : angle       1.11815 (   12)
  hydrogen bonds       : bond        0.03193 (   73)
  hydrogen bonds       : angle       6.01380 (  177)
  link_NAG-ASN         : bond        0.00261 (    2)
  link_NAG-ASN         : angle       3.06937 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 74
  average time/residue: 0.1672
  time to fit residues: 14.6373
Evaluate side-chains
  73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  42 GLN
** C   3 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 = 0.4003 r_free = 0.4003 target = 0.176875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.153055 restraints weight = 12390.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.159066 restraints weight = 6433.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.163038 restraints weight = 4082.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.165568 restraints weight = 2893.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.167418 restraints weight = 2229.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3648  Z= 0.163
  Angle     :  0.598  10.651   4971  Z= 0.302
  Chirality :  0.088   1.762    538
  Planarity :  0.004   0.059    640
  Dihedral  :  6.465  53.785    541
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.55 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.17 (0.37), residues: 443
  helix: -2.51 (0.80), residues: 27
  sheet: -1.38 (0.49), residues: 103
  loop : -1.42 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  61 
 TYR   0.014   0.001   TYR B  49 
 PHE   0.008   0.001   PHE A 429 
 TRP   0.006   0.001   TRP C 100B
 HIS   0.004   0.002   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3640)
  covalent geometry    : angle       0.58412 ( 4953)
  SS BOND              : bond        0.00525 (    6)
  SS BOND              : angle       1.03896 (   12)
  hydrogen bonds       : bond        0.03301 (   73)
  hydrogen bonds       : angle       5.95165 (  177)
  link_NAG-ASN         : bond        0.00364 (    2)
  link_NAG-ASN         : angle       3.49362 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 76
  average time/residue: 0.1765
  time to fit residues: 15.9303
Evaluate side-chains
  72 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0770
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
B  42 GLN
C   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.177745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.154658 restraints weight = 12392.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.160596 restraints weight = 6519.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.164363 restraints weight = 4142.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.166932 restraints weight = 2955.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.168581 restraints weight = 2263.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3648  Z= 0.120
  Angle     :  0.566  10.390   4971  Z= 0.283
  Chirality :  0.087   1.736    538
  Planarity :  0.004   0.068    640
  Dihedral  :  6.102  50.633    541
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.55 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.10 (0.38), residues: 443
  helix: -2.53 (0.79), residues: 27
  sheet: -1.49 (0.46), residues: 120
  loop : -1.26 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  61 
 TYR   0.014   0.001   TYR B  49 
 PHE   0.006   0.001   PHE A 497 
 TRP   0.007   0.001   TRP C 100B
 HIS   0.003   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3640)
  covalent geometry    : angle       0.55522 ( 4953)
  SS BOND              : bond        0.00470 (    6)
  SS BOND              : angle       0.82682 (   12)
  hydrogen bonds       : bond        0.03028 (   73)
  hydrogen bonds       : angle       5.78043 (  177)
  link_NAG-ASN         : bond        0.00211 (    2)
  link_NAG-ASN         : angle       3.08198 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  425 LEU cc_start: 0.9132 (mt) cc_final: 0.8731 (mt)
  outliers start: 4
  outliers final: 4
  residues processed: 74
  average time/residue: 0.1719
  time to fit residues: 15.1747
Evaluate side-chains
  73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain C residue    3 GLN
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 26 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    0.2980
   chunk 28 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
B  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.177631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.154653 restraints weight = 12403.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.160472 restraints weight = 6591.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.164319 restraints weight = 4215.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.166807 restraints weight = 2992.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.168586 restraints weight = 2298.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3648  Z= 0.133
  Angle     :  0.578  11.312   4971  Z= 0.289
  Chirality :  0.086   1.704    538
  Planarity :  0.004   0.072    640
  Dihedral  :  6.149  51.722    541
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.81 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.09 (0.38), residues: 443
  helix: -2.53 (0.80), residues: 27
  sheet: -1.45 (0.46), residues: 120
  loop : -1.26 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  61 
 TYR   0.014   0.001   TYR B  49 
 PHE   0.006   0.001   PHE A 490 
 TRP   0.007   0.001   TRP C 100B
 HIS   0.003   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3640)
  covalent geometry    : angle       0.56686 ( 4953)
  SS BOND              : bond        0.00461 (    6)
  SS BOND              : angle       0.85532 (   12)
  hydrogen bonds       : bond        0.03064 (   73)
  hydrogen bonds       : angle       5.74347 (  177)
  link_NAG-ASN         : bond        0.00260 (    2)
  link_NAG-ASN         : angle       3.11696 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  425 LEU cc_start: 0.9145 (mt) cc_final: 0.8744 (mt)
REVERT: A  529 LYS cc_start: 0.7188 (tmtt) cc_final: 0.6959 (tmtt)
  outliers start: 3
  outliers final: 3
  residues processed: 71
  average time/residue: 0.1855
  time to fit residues: 15.7259
Evaluate side-chains
  71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0870
   chunk 35 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
B  42 GLN
** C   3 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 = 0.4008 r_free = 0.4008 target = 0.177398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.154498 restraints weight = 12289.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.160251 restraints weight = 6536.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.164124 restraints weight = 4177.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.166613 restraints weight = 2970.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.168181 restraints weight = 2279.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3648  Z= 0.130
  Angle     :  0.570  10.232   4971  Z= 0.285
  Chirality :  0.088   1.758    538
  Planarity :  0.005   0.075    640
  Dihedral  :  6.013  51.860    541
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.81 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.05 (0.38), residues: 443
  helix: -2.49 (0.80), residues: 27
  sheet: -1.42 (0.46), residues: 120
  loop : -1.23 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  61 
 TYR   0.014   0.001   TYR B  49 
 PHE   0.006   0.001   PHE A 490 
 TRP   0.007   0.001   TRP C 100B
 HIS   0.003   0.002   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3640)
  covalent geometry    : angle       0.55908 ( 4953)
  SS BOND              : bond        0.00472 (    6)
  SS BOND              : angle       0.87948 (   12)
  hydrogen bonds       : bond        0.02989 (   73)
  hydrogen bonds       : angle       5.66478 (  177)
  link_NAG-ASN         : bond        0.00241 (    2)
  link_NAG-ASN         : angle       3.14653 (    6)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 LYS cc_start: 0.7182 (tmtt) cc_final: 0.6950 (tmtt)
  outliers start: 3
  outliers final: 3
  residues processed: 72
  average time/residue: 0.1801
  time to fit residues: 15.5339
Evaluate side-chains
  71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0040
   chunk 27 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
B  42 GLN
C   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.175478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152809 restraints weight = 12429.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.158670 restraints weight = 6543.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.162406 restraints weight = 4137.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.164909 restraints weight = 2941.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.166616 restraints weight = 2247.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3648  Z= 0.153
  Angle     :  0.595  10.399   4971  Z= 0.296
  Chirality :  0.088   1.748    538
  Planarity :  0.005   0.074    640
  Dihedral  :  6.087  53.149    541
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.81 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.06 (0.38), residues: 443
  helix: -2.47 (0.81), residues: 27
  sheet: -1.59 (0.49), residues: 110
  loop : -1.19 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  61 
 TYR   0.015   0.001   TYR B  49 
 PHE   0.007   0.001   PHE A 490 
 TRP   0.007   0.001   TRP C 100B
 HIS   0.003   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 3640)
  covalent geometry    : angle       0.58303 ( 4953)
  SS BOND              : bond        0.00501 (    6)
  SS BOND              : angle       0.92129 (   12)
  hydrogen bonds       : bond        0.03099 (   73)
  hydrogen bonds       : angle       5.67820 (  177)
  link_NAG-ASN         : bond        0.00327 (    2)
  link_NAG-ASN         : angle       3.38606 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1968.22 seconds
wall clock time: 34 minutes 3.96 seconds (2043.96 seconds total)